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(-) Description

Title :  STRUCTURE OF SMALL TOPRIM DOMAIN-CONTAINING PROTEIN FROM B. STEAROTHERMOPHILUS IN COMPLEX WITH MG2+
 
Authors :  P. Rezacova, D. Borek, Z. Otwinowski, A. Joachimiak, S. F. Moy, Midwest For Structural Genomics (Mcsg)
Date :  25 Aug 06  (Deposition) - 03 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Toprim Domain, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Rezacova, D. Borek, S. F. Moy, A. Joachimiak, Z. Otwinowski
Crystal Structure And Putative Function Of Small Toprim Domain-Containing Protein From Bacillus Stearothermophilus.
Proteins V. 70 311 2007
PubMed-ID: 17705269  |  Reference-DOI: 10.1002/PROT.21511

(-) Compounds

Molecule 1 - TOPRIM DOMAIN-CONTAINING PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MG2Ligand/IonMAGNESIUM ION
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MES-1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MES-1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (3, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4SO42Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:58 , ASP A:60 , GLU A:88 , HOH A:442 , HOH A:443 , HOH A:468BINDING SITE FOR RESIDUE MG A 301
02AC2SOFTWAREASP B:58 , ASP B:60 , HOH B:414 , HOH B:438BINDING SITE FOR RESIDUE MG B 302
03AC3SOFTWAREARG B:3 , HIS C:96 , GLN C:99 , ARG C:103 , ARG C:115BINDING SITE FOR RESIDUE SO4 C 501
04AC4SOFTWARELYS C:65 , ARG C:68 , ARG C:109 , HOH C:621BINDING SITE FOR RESIDUE SO4 C 502
05AC5SOFTWAREGLU C:11 , GLY C:12 , ASP C:58 , ASP C:60 , GLU C:61 , ALA C:62 , ARG C:87 , GLU C:88 , HOH C:615 , HOH C:652 , HOH C:678 , HOH C:679 , HOH C:683 , HOH C:685BINDING SITE FOR RESIDUE MES C 601
06AC6SOFTWARELEU A:23 , GLU A:25 , PRO A:26 , VAL A:27 , ILE A:29 , HOH A:453BINDING SITE FOR RESIDUE GOL A 400
07AC7SOFTWAREGLU A:64 , ARG A:67 , ARG A:71 , TYR A:81 , HOH A:451 , LEU C:48 , GLY C:50 , TYR C:51 , VAL C:53 , PHE C:74BINDING SITE FOR RESIDUE GOL A 404
08AC8SOFTWARELEU B:102 , ARG B:103 , HOH B:413 , LEU C:23 , GLU C:25 , PRO C:26 , VAL C:27 , ILE C:29BINDING SITE FOR RESIDUE GOL B 401
09AC9SOFTWAREASN B:24 , ASP B:107 , VAL B:108 , HOH B:407 , HOH B:422 , VAL C:28 , ILE C:29BINDING SITE FOR RESIDUE GOL B 403
10BC1SOFTWAREGLU B:47 , HOH B:409 , THR C:35 , ILE C:36 , LYS C:65 , LEU C:66 , GLN C:69 , GLU C:111BINDING SITE FOR RESIDUE GOL C 402
11BC2SOFTWAREHOH B:435 , ALA C:59 , GLU C:64 , ARG C:84BINDING SITE FOR RESIDUE GOL C 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I5R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I5R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I5R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2I5R)

(-) Exons   (0, 0)

(no "Exon" information available for 2I5R)

(-) 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:115
 aligned with Q5KVJ9_GEOKA | Q5KVJ9 from UniProtKB/TrEMBL  Length:119

    Alignment length:115
                             1                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109     
         Q5KVJ9_GEOKA     - -MRRVEKVIIVEGRSDKQKVAAVLNEPVVIVCTNGTISDARLEELADELEGCDVYVLADADEAGEKLRRQFRRMFPEAEHLYIDRAYREVAAAPPWHLAQVLLRARFDVRIESLM 114
               SCOP domains d2i5ra_ A: automated matches                                                                                        SCOP domains
               CATH domains 2i5rA00 A:0-114 Toprim domain                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.hhhhhhhhhhhh....eeee.....hhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhh....hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2i5r A   0 AMRRVEKVIIVEGRSDKQKVAAVLNEPVVIVCTNGTISDARLEELADELEGYDVYLLADADEAGEKLRRQFRRMFPEAEHLYIDRAYREVAAAPIWHLAQVLLRARFDVRIESLM 114
                                     9        19        29        39        49        59        69        79        89        99       109     


Chain B from PDB  Type:PROTEIN  Length:118
 aligned with Q5KVJ9_GEOKA | Q5KVJ9 from UniProtKB/TrEMBL  Length:119

    Alignment length:118
                                    11        21        31        41        51        61        71        81        91       101       111        
         Q5KVJ9_GEOKA     2 RRVEKVIIVEGRSDKQKVAAVLNEPVVIVCTNGTISDARLEELADELEGCDVYVLADADEAGEKLRRQFRRMFPEAEHLYIDRAYREVAAAPPWHLAQVLLRARFDVRIESLMRGRGE 119
               SCOP domains d2i5rb_ B: automated matches                                                                                           SCOP domains
               CATH domains 2i5rB00 B:2-119 Toprim domain                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.hhhhhhhhhhhh....eeee.....hhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhhh....hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2i5r B   2 RRVEKVIIVEGRSDKQKVAAVLNEPVVIVCTNGTISDARLEELADELEGYDVYLLADADEAGEKLRRQFRRMFPEAEHLYIDRAYREVAAAPIWHLAQVLLRARFDVRIESLMRGRGE 119
                                    11        21        31        41        51        61        71        81        91       101       111        


Chain C from PDB  Type:PROTEIN  Length:117
 aligned with Q5KVJ9_GEOKA | Q5KVJ9 from UniProtKB/TrEMBL  Length:119

    Alignment length:117
                                    10        20        30        40        50        60        70        80        90       100       110       
         Q5KVJ9_GEOKA     1 MRRVEKVIIVEGRSDKQKVAAVLNEPVVIVCTNGTISDARLEELADELEGCDVYVLADADEAGEKLRRQFRRMFPEAEHLYIDRAYREVAAAPPWHLAQVLLRARFDVRIESLMRGR 117
               SCOP domains d2i5rc_ C: automated matches                                                                                          SCOP domains
               CATH domains 2i5rC00 C:1-117 Toprim domain                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.hhhhhhhhhhhh....eeee.....hhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhhh....hhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2i5r C   1 MRRVEKVIIVEGRSDKQKVAAVLNEPVVIVCTNGTISDARLEELADELEGYDVYLLADADEAGEKLRRQFRRMFPEAEHLYIDRAYREVAAAPIWHLAQVLLRARFDVRIESLMRGR 117
                                    10        20        30        40        50        60        70        80        90       100       110
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I5R)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q5KVJ9_GEOKA | Q5KVJ9)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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

UniProtKB/TrEMBL
        Q5KVJ9_GEOKA | Q5KVJ9: 2fcj

(-) Related Entries Specified in the PDB File

2fcj TRUCTURE OF SMALL TOPRIM DOMAIN-CONTAINING PROTEIN FROM B. STEAROTHERMOPHILUS RELATED ID: APC35832 RELATED DB: TARGETDB