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(-) Description

Title :  STRUCTURE OF BACTEROIDES SP PIF1 COMPLEXED WITH TAILED DSDNA RESULTING IN SSDNA BOUND COMPLEX
 
Authors :  X. Zhou, W. Ren, S. R. Bharath, H. Song
Date :  22 Dec 15  (Deposition) - 30 Mar 16  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,E
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,E  (1x)
Keywords :  Pif1 Helicase, Dna Helicase, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhou, W. Ren, S. R. Bharath, X. Tang, Y. He, C. Chen, Z. Liu, D. Li, H. Song
Structural And Functional Insights Into The Unwinding Mechanism Of Bacteroides Sp Pif1
Cell Rep V. 14 2030 2016
PubMed-ID: 26904952  |  Reference-DOI: 10.1016/J.CELREP.2016.02.008

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HMPREF0101_01022
    Organism Scientific: BACTEROIDES SP. 2_1_16
    Organism Taxid: 469587
    Synonym: PIF1
 
Molecule 2 - DNA (5'- D(*TP*TP*TP*TP*TP*TP*TP*CP*CP*GP*GP*GP*GP*CP*CP*GP*CP*GP*C)-3')
    Chains: C, E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCE
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ALF2Ligand/IonTETRAFLUOROALUMINATE ION
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ALF1Ligand/IonTETRAFLUOROALUMINATE ION
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ALF1Ligand/IonTETRAFLUOROALUMINATE ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:4 , ILE A:5 , GLY A:31 , SER A:32 , GLY A:33 , LYS A:34 , THR A:35 , THR A:36 , PHE A:187 , ARG A:188 , THR A:367 , ARG A:392 , MG A:502 , ALF A:503 , HOH A:627 , HOH A:655 , HOH A:677 , HOH A:722 , HOH A:732binding site for residue ADP A 501
2AC2SOFTWARETHR A:35 , ADP A:501 , ALF A:503 , HOH A:655 , HOH A:656 , HOH A:660binding site for residue MG A 502
3AC3SOFTWAREALA A:30 , GLY A:31 , LYS A:34 , GLU A:106 , GLN A:145 , ARG A:188 , GLY A:365 , ARG A:390 , ADP A:501 , MG A:502 , HOH A:616 , HOH A:626 , HOH A:655 , HOH A:656 , HOH A:660binding site for residue ALF A 503
4AC4SOFTWAREGLU B:2 , ASP B:3 , MET B:4 , ILE B:5 , MET B:10 , GLY B:31 , SER B:32 , GLY B:33 , LYS B:34 , THR B:35 , THR B:36 , PHE B:187 , ARG B:188 , THR B:367 , ARG B:392 , MG B:502 , ALF B:503 , HOH B:617 , HOH B:620 , HOH B:696 , HOH B:720binding site for residue ADP B 501
5AC5SOFTWARETHR B:35 , ADP B:501 , ALF B:503 , HOH B:617 , HOH B:659 , HOH B:674binding site for residue MG B 502
6AC6SOFTWAREALA B:30 , GLY B:31 , LYS B:34 , GLU B:106 , GLN B:145 , ARG B:188 , GLY B:365 , ARG B:390 , ADP B:501 , MG B:502 , HOH B:619 , HOH B:641 , HOH B:659 , HOH B:674binding site for residue ALF B 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:342 -Glu A:343

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FHD)

(-) 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:414
                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh...eeeee.hhhhhhhhh.eehhhhhh................hhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhheeeeee.........hhhhhhhhh......hhhhhhhhhh.eeeeeee.......hhhhhhhhhhhhh...hhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhh....eeee.eee...hhhhh....eeee....eeee...hhhhh.....eeeeeee....eeeee....eeee..eeeee....eeeee..eee...eehhhhh......eeee.......hhhhhhhhh......eee....hhhhh..hhhhhhhhhhhhhh..eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fhd A   3 DMILTEEMQKIMNLIQDDENNVFVTGKAGSGKTTFLKYLIEKSGKNCIVAAPTGIAAINAGGVTLHSLFGIPFGPITPYDRLENKFSEYKVELLLKMELLIIDEISMVRPDILDTIDRKLRWVYESDEPFGGVQVVMFGDLFQLPPVTKKQEREILSDFYDGFFFFNALVFKRTGFHIVELTKIFRQTEPEFINVLNNIRNYQVTSDELDLLSELKDRKINEYIHICTHKADVEKINADKLGEQEIRNYDIVIKDKFPESSIPCDLHLKLRVGARVMSLVNDSLKGYYNGMLGIVTALEDNVITVRMDNGRTIKFERYTWSNTEEIGSCTQFPLTLAWAITIHKSQGLTFDKIIIHVSHTFCPGQLYVALSRCRTLEGIVSDAFITKQMIIPEYALIDFERAYKSEGNYYGKRL 432
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222|      237       247       257       267       277       287       297       307       317       327  ||   348       358       368       378       388       398       408       418       428    
                                                                                                                                                                                                                                                     222|                                                                                                   330|                                                                                          
                                                                                                                                                                                                                                                      228                                                                                                    342                                                                                          


Chain B from PDB  Type:PROTEIN  Length:400
                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh...eeeee.hhhhhhhhh.eehhhhhh................hhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhheeeee..........hhhhhhhhhh.....hhhhhhhhhh.eeeeeee.......hhhhhhhhhhhhh...hhhhhhhhhhhh.....ee.....eeee.hhhhhhhhhhhhhh...ee...........ee...eeee...........eeee.......eee....ee....eee..eee..eee..eeehhhhh......eeee.......hhhhhhhhh......eee....hhhhh..hhhhhhhhhhhhhh..eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fhd B   1 MEDMILTEEMQKIMNLIQDDENNVFVTGKAGSGKTTFLKYLIEKSGKNCIVAAPTGIAAINAGGVTLHSLFGIPFGPITPYDRLENKFSEYKVELLLKMELLIIDEISMVRPDILDTIDRKLRWVYESDEPFGGVQVVMFGDLFQLPPVTKKQEREILSDFYDGFFFFNALVFKRTGFHIVELTKIFRQTEPEFINVLNNIRNYQVTSDELDLLSELKDRKISSSYDNEYIHICTHKADVEKINADKLGQEIRNYDIVSIPCDLHLKLRARVMSLVNDSLYYNGMLGIVTALEDNTVRMDNGRTIKFERYTWSSCTQFPLTLAWAITIHKSQGLTFDKIIIHVSHTFCPGQLYVALSRCRTLEGIVSDAFITKQMIIPEYALIDFERAYKSEGNYYGKRL 432
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       251       269       281       291|      303    || 315       325  ||   352       362       372       382       392       402       412       422       432
                                                                                                                                                                                                                                                                                  249|     259|       278|       291|           308|              328|                                                                                      
                                                                                                                                                                                                                                                                                   251      268        281        294            311               346                                                                                      


Chain C from PDB  Type:DNA  Length:8
                                        
                 5fhd C   3 TTTTTCCG  10


Chain E from PDB  Type:DNA  Length:7
                                       
                 5fhd E   3 TTTTTTC   9
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5FHD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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        D1JM21_9BACE | D1JM21: 5fhe 5fhf 5fhg

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5fhe 5fhf 5fhg 5fhh