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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LGRA INITIATION MODULE EXCLUDING THE ASUB DOMAIN: F-A-DELTA-SUB
 
Authors :  J. M. Reimer, M. N. Aloise, T. M. Schmeing
Date :  29 Apr 16  (Deposition) - 12 Oct 16  (Release) - 12 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Nrps, Formylation Domain, Adenylation Domain, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Reimer, M. N. Aloise, H. R. Powell, T. M. Schmeing
Manipulation Of An Existing Crystal Form Unexpectedly Results In Interwoven Packing Networks With Pseudo-Translational Symmetry
Acta Crystallogr. , Sect. D V. 72 1130 2016
PubMed: search  |  Reference-DOI: 10.1107/S2059798316013504

(-) Compounds

Molecule 1 - LINEAR GRAMICIDIN SYNTHASE SUBUNIT A
    Chains: C, A, B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2-584
    Gene: LGRA
    Organism Scientific: BREVIBACILLUS PARABREVIS
    Organism Taxid: 54914

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):   C 
Biological Unit 2 (1x): A   
Biological Unit 3 (1x):  B  
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1FMT5Ligand/IonFORMIC ACID
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1FMT4Ligand/IonFORMIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1FMT-1Ligand/IonFORMIC ACID
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1FMT-1Ligand/IonFORMIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY C:54 , ARG C:83 , LYS C:167binding site for residue FMT C 601
2AC2SOFTWAREARG C:83 , ASP C:84binding site for residue FMT C 602
3AC3SOFTWARETYR C:55 , LEU C:57binding site for residue FMT C 603
4AC4SOFTWAREASP C:396 , TYR C:439 , GLY C:482binding site for residue FMT C 604
5AC5SOFTWARETYR A:55 , LEU A:57binding site for residue FMT A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JNF)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu C:77 -Pro C:78
2Leu A:77 -Pro A:78
3Leu B:77 -Pro B:78
4Leu D:77 -Pro D:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JNF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JNF)

(-) Exons   (0, 0)

(no "Exon" information available for 5JNF)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:585
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......hhhhhhhhhh..eeeee.......hhhhh...eeeee......hhhhhhhh...eeeee.......ee.hhhhhhhhh....eeeeee.........eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh.............eehhhhhhhhhhhh..hhhhhhhhhhhhh...........hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhh...eeee...hhhhhh...eeee..hhhhh...............eeeeee.........eeeeehhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhh...eeee.hhhhh.hhhhhhhhhhhhh..eeeeehhhhhhhh........eeeee.............eeeeee.hhhhh...eeeee..........ee...eeeeee............eeeeeee.....ee..hhhhhhhheee......eeeeeeeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jnf A   1 MGRILFLTTFMSKGNKVVRYLESLHHEVVICQEKVHAQSANLQEIDWIVSYAYGYILDKEIVSRFRGRIINLHPSLLPWNKGRDPVFWSVWDETPKGVTIHLIDEHVDTGDILVQEEIAFADEDTLLDCYNKANQAIEELFIREWENIVHGRIAPYRQTAGGTLHFKADRDFYKNLNMTTVRELLALKRLCAEPKRGEKPIDKTFHQLFEQQVEMTPDHVAVVDRGQSLTYKQLNERANQLAHHLRGKGVKPDDQVAIMLDKSLDMIVSILAVMKAGGAYVPIDPDYPGERIAYMLADSSAAILLTNALHEEKANGACDIIDVHDPDSYSENTNNLPHVNRPDDLVYVMYTSGSTGLAKGVMIEHHNLVNFCEWYRPYFGVTPADKALVYSSFSFDGSALDIFTHLLAGAALHIVPSERKYDLDALNDYCNQEGITISYLPTGAAEQFMQMDNQSFRVVITGGDVLKKIERNGTYKLYNGYGPTECTIMVTMFEVDKPYANIPIGKPIDRTRILILDEALALQPIGVAGELFIVGEGLGRGYLNRPELTAEKFIVHPQTGERMYRTGDRARFLPDGNIEFLGRLD 585
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580     


Chain B from PDB  Type:PROTEIN  Length:580
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhh...eeee.......hhhhh...eeeee......hhhhhhhh...eeeee.......ee.hhhhhhhhh....eeeeee.........eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh.............eehhhhhhhhh.....hhhhhhhhhhhhh...........hhhhhhhhhhh.....eeeee..eeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhh...eeee...hhhhhh...eeee..hhhhh...............eeeeee....eeeeehhhhhhhhhhhhhhh......eeee......hhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh..eeeeehhhhhhhh........eeeee.............eeeeee.hhhhh...eeee...........ee...eeeeee............eeeeeee.....ee..hhhhhhhheee......eeeeeeeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jnf B   1 MGRILFLTTFMSKGNKVVRYLESLHHEVVICQEKVHAQSANLQEIDWIVSYAYGYILDKEIVSRFRGRIINLHPSLLPWNKGRDPVFWSVWDETPKGVTIHLIDEHVDTGDILVQEEIAFADEDTLLDCYNKANQAIEELFIREWENIVHGRIAPYRQTAGGTLHFKADRDFYKNLNMTTVRELLALKRLCAEPKRGEKPIDKTFHQLFEQQVEMTPDHVAVVDRGQSLTYKQLNERANQLAHHLRGKGVKPDDQVAIMLDKSLDMIVSILAVMKAGGAYVPIDPDYPGERIAYMLADSSAAILLTNALHEEKANGACDIIDVHDPDSYSENTNNLPHVNRPDDLVYVMYTLAKGVMIEHHNLVNFCEWYRPYFGVTPADKALVYSSFSFDGSALDIFTHLLAGAALHIVPSERKYDLDALNDYCNQEGITISYLPTGAAEQFMQMDNQSFRVVITGGDVLKKIERNGTYKLYNGYGPTECTIMVTMFEVDKPYANIPIGKPIDRTRILILDEALALQPIGVAGELFIVGEGLGRGYLNRPELTAEKFIVHPQTGERMYRTGDRARFLPDGNIEFLGRLD 585
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350||     365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585
                                                                                                                                                                                                                                                                                                                                                                                        351|                                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                                                                                                                                         357                                                                                                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:583
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......hhhhhhhhhh..eeeee.......hhhhh...eeeee......hhhhhhhh...eeeee.......ee.hhhhhhhhh....eeeeee.........eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh.............eehhhhhhhhhhhh..hhhhhhhhhhhhh...........hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhh...eeee...hhhhhh...eeee..hhhhh...............eeeeeee.....eeeeeehhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhh.eeee.hhhhh.hhhhhhhhhhhhh..eeeeehhhhhhhh........eeeee.............eeeeee.hhhhh...eeeee..........ee...eeeeee............eeeeeee.....ee..hhhhhhhheee......eeeeeeeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jnf C   1 MGRILFLTTFMSKGNKVVRYLESLHHEVVICQEKVHAQSANLQEIDWIVSYAYGYILDKEIVSRFRGRIINLHPSLLPWNKGRDPVFWSVWDETPKGVTIHLIDEHVDTGDILVQEEIAFADEDTLLDCYNKANQAIEELFIREWENIVHGRIAPYRQTAGGTLHFKADRDFYKNLNMTTVRELLALKRLCAEPKRGEKPIDKTFHQLFEQQVEMTPDHVAVVDRGQSLTYKQLNERANQLAHHLRGKGVKPDDQVAIMLDKSLDMIVSILAVMKAGGAYVPIDPDYPGERIAYMLADSSAAILLTNALHEEKANGACDIIDVHDPDSYSENTNNLPHVNRPDDLVYVMYTSTGLAKGVMIEHHNLVNFCEWYRPYFGVTPADKALVYSSFSFDGSALDIFTHLLAGAALHIVPSERKYDLDALNDYCNQEGITISYLPTGAAEQFMQMDNQSFRVVITGGDVLKKIERNGTYKLYNGYGPTECTIMVTMFEVDKPYANIPIGKPIDRTRILILDEALALQPIGVAGELFIVGEGLGRGYLNRPELTAEKFIVHPQTGERMYRTGDRARFLPDGNIEFLGRLD 585
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 ||    362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582   
                                                                                                                                                                                                                                                                                                                                                                                         352|                                                                                                                                                                                                                                      
                                                                                                                                                                                                                                                                                                                                                                                          355                                                                                                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:581
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......hhhhhhhhhh..eeeee.......hhhhh...eeeee......hhhhhhhh...eeeee.......ee.hhhhhhhhh....eeeeee.........eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh.............eehhhhhhhhhhhh..hhhhhhhhhhhhh...........hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhh...eeee...hhhhhh...eeee..hhhhh...............eeeeeee...eeeeeehhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhh..eeee.hhhhh.hhhhhhhhhhhhh..eeeeehhhhhhhh........eeeee.............eeeeee.hhhhh...eeeee..........ee...eeeeee............eeeeeee.....ee..hhhhhhhheee......eeeeeeeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jnf D   1 MGRILFLTTFMSKGNKVVRYLESLHHEVVICQEKVHAQSANLQEIDWIVSYAYGYILDKEIVSRFRGRIINLHPSLLPWNKGRDPVFWSVWDETPKGVTIHLIDEHVDTGDILVQEEIAFADEDTLLDCYNKANQAIEELFIREWENIVHGRIAPYRQTAGGTLHFKADRDFYKNLNMTTVRELLALKRLCAEPKRGEKPIDKTFHQLFEQQVEMTPDHVAVVDRGQSLTYKQLNERANQLAHHLRGKGVKPDDQVAIMLDKSLDMIVSILAVMKAGGAYVPIDPDYPGERIAYMLADSSAAILLTNALHEEKANGACDIIDVHDPDSYSENTNNLPHVNRPDDLVYVMYTSGAKGVMIEHHNLVNFCEWYRPYFGVTPADKALVYSSFSFDGSALDIFTHLLAGAALHIVPSERKYDLDALNDYCNQEGITISYLPTGAAEQFMQMDNQSFRVVITGGDVLKKIERNGTYKLYNGYGPTECTIMVTMFEVDKPYANIPIGKPIDRTRILILDEALALQPIGVAGELFIVGEGLGRGYLNRPELTAEKFIVHPQTGERMYRTGDRARFLPDGNIEFLGRLD 585
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350  ||   364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584 
                                                                                                                                                                                                                                                                                                                                                                                          353|                                                                                                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                                                                                           358
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5JNF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JNF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JNF)

(-) Gene Ontology  (7, 7)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        LGRA_BREPA | Q70LM7: 5es5 5es6 5es7 5es8 5es9

(-) Related Entries Specified in the PDB File

5es5 5es6 5es7 5es8 5es9