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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE TRANSCRIPTIONAL REPRESSOR OF RIBOSE OPERON FROM STAPHYLOCOCCUS SAPROPHYTICUS SUBSP. SAPROPHYTICUS
 
Authors :  J. B. Bonanno, J. Freeman, K. T. Bain, S. Chang, R. Romero, D. Smith, S. Wa J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center Structural Genomics (Nysgxrc)
Date :  14 Aug 08  (Deposition) - 26 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Structural Genomics, Transcription, Dna-Binding, Transcription Regulation, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Bonanno, J. Freeman, K. T. Bain, S. Chang, R. Romero, D. Smith, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of A Putative Transcriptional Repressor O Ribose Operon From Staphylococcus Saprophyticus Subsp. Saprophyticus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE TRANSCRIPTIONAL REPRESSOR OF RIBOSE OPERON
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: SSP1396
    Organism Scientific: STAPHYLOCOCCUS SAPROPHYTICUS SUBSP. SAPROPHYTICUS
    Organism Taxid: 342451
    Strain: ATCC 15305

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB
Biological Unit 2 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:71 , PHE A:73 , PHE A:188 , ARG A:191 , ASN A:236 , ASP A:264 , GLN A:281BINDING SITE FOR RESIDUE GOL A 1
2AC2SOFTWAREASN B:71 , PHE B:73 , PHE B:188 , ARG B:191 , ASN B:236 , ASP B:264 , GLN B:281 , HOH B:343BINDING SITE FOR RESIDUE GOL B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E61)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Val A:254 -Pro A:255
2Tyr A:273 -Pro A:274
3Val B:254 -Pro B:255
4Tyr B:273 -Pro B:274

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E61)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E61)

(-) Exons   (0, 0)

(no "Exon" information available for 3E61)

(-) 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:239
 aligned with Q49XF6_STAS1 | Q49XF6 from UniProtKB/TrEMBL  Length:321

    Alignment length:266
                                                                                                                                                                                                                                                                                              321     
                                    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|     
         Q49XF6_STAS1    61 LIGLLLPDMSNPFFTLIARGVEDVALAHGYQVLIGNSDNDIKKAQGYLATFVSHNCTGMISTAFNENIIENTLTDHHIPFVFIDRINNEHNGISTNHFKGGQLQAEVVRKGKGKNVLIVHENLLIDAFHQRVQGIKYILDQQRIDYKMLEATLLDNDKKFIDLIKELSIDSIICSNDLLAINVLGIVQRYHFKVPAEIQIIGYDNIPFSEMTYPQITTIDQSAYHLGEIAVSQLLGLNTDNLTNNHKQLALTVKHRGSTRN-----   -
               SCOP domains d3e61a_ A: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh-..eee.hhh---------hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh---.eeeee.hhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh........eee....hhhhhh......eee.hhhhhhhhhhhhhh--------------..eee............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e61 A  61 LIGLLLPDMSNPFFTLIARGVEDVALAHGYQVLIGNSDNDIKKAQGYLATFVSHNCTGMISTAFNENIIENTLTDH-IPFVFIDRI---------NHFKGGQLQAEVVRKGKGKNVLIVHENLLIDAFHQRVQGIKYILDQ---DYKMLEATLLDNDKKFIDLIKELSIDSIICSNDLLAINVLGIVQRYHFKVPAEIQIIGYDNIPFSEMTYPQITTIDQSAYHLGEIAVSQLL--------------ALTVKHRGSTRHHHHHH 328
                                    70        80        90       100       110       120       130     | 140     |   -     | 160       170       180       190       200|   |  210       220       230       240       250       260       270       280       290    |    -       310       320|     
                                                                                                     136 |     146       156                                          201 205                                                                                       295            310       320|     
                                                                                                       138                                                                                                                                                                                    323     


Chain B from PDB  Type:PROTEIN  Length:241
 aligned with Q49XF6_STAS1 | Q49XF6 from UniProtKB/TrEMBL  Length:321

    Alignment length:260
                                    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
         Q49XF6_STAS1    61 LIGLLLPDMSNPFFTLIARGVEDVALAHGYQVLIGNSDNDIKKAQGYLATFVSHNCTGMISTAFNENIIENTLTDHHIPFVFIDRINNEHNGISTNHFKGGQLQAEVVRKGKGKNVLIVHENLLIDAFHQRVQGIKYILDQQRIDYKMLEATLLDNDKKFIDLIKELSIDSIICSNDLLAINVLGIVQRYHFKVPAEIQIIGYDNIPFSEMTYPQITTIDQSAYHLGEIAVSQLLGLNTDNLTNNHKQLALTVKHRGSTR 320
               SCOP domains d3e61b_ B: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh...eee..------.....hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhh........eee....hhhhhh......eee.hhhhhhhhhhhhhhh-------------..eee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e61 B  61 LIGLLLPDMSNPFFTLIARGVEDVALAHGYQVLIGNSDNDIKKAQGYLATFVSHNCTGMISTAFNENIIENTLTDHHIPFVFID------NGISTNHFKGGQLQAEVVRKGKGKNVLIVHENLLIDAFHQRVQGIKYILDQQRIDYKMLEATLLDNDKKFIDLIKELSIDSIICSNDLLAINVLGIVQRYHFKVPAEIQIIGYDNIPFSEMTYPQITTIDQSAYHLGEIAVSQLLG-------------ALTVKHRGSTR 320
                                    70        80        90       100       110       120       130       140   |     -|      160       170       180       190       200       210       220       230       240       250       260       270       280       290     |   -       310       320
                                                                                                             144    151                                                                                                                                              296           310
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E61)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E61)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q49XF6_STAS1 | Q49XF6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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  3e61
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