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(-) Description

Title :  THE CRYSTAL STRUCTURE OF TRANSCRIPTION REGULATOR GNTR FROM CHROMOBACTERIUM VIOLACEUM
 
Authors :  Z. Zhang, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  22 Apr 09  (Deposition) - 05 May 09  (Release) - 05 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  11234B, Transcription Regulator, Gntr, Chromobacterium Violaceum, Psi, Sgx, Dna-Binding, Transcription, Transcription Regulation, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, S. K. Burley, S. Swaminathan
The Crystal Structure Of Transcription Regulator Gntr From Chromobacterium Violaceum
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR GNTR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX(BC)
    Expression System Strain: BL21(DE3)-CODON+RIL-STRATAGENE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CV_2956, GNTR
    Organism Scientific: CHROMOBACTERIUM VIOLACEUM
    Organism Taxid: 536

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 18)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:79 , LEU A:80 , ALA A:81 , ASN A:107 , HIS A:109BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWARESER B:79 , LEU B:80 , ALA B:81 , ASN B:107 , HIS B:109BINDING SITE FOR RESIDUE SO4 B 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H5O)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Val A:273 -Pro A:274
2Thr A:292 -Pro A:293
3Val B:273 -Pro B:274
4Thr B:292 -Pro B:293

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H5O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H5O)

(-) Exons   (0, 0)

(no "Exon" information available for 3H5O)

(-) 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:271
 aligned with Q7NTU7_CHRVO | Q7NTU7 from UniProtKB/TrEMBL  Length:339

    Alignment length:271
                                                                                                                                                                                                                                                                                                      339  
                                    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        |- 
         Q7NTU7_CHRVO    71 RTVLVLIPSLANTVFLETLTGIETVLDAAGYQMLIGNSHYDAGQELQLLRAYLQHRPDGVLITGLSHAEPFERILSQHALPVVYMMDLADDGRCCVGFSQEDAGAAITRHLLSRGKRRIGFLGAQLDERVMKRLDGYRAALDAADCRDAGLEWLDPQPSSMQMGADMLDRALAERPDCDALFCCNDDLAIGALARSQQLGIAVPERLAIAGFNDLQPAAWCTPPLTTVATPRRDIGVHAAKALLQLIDGEEPASRRADLGFRLMLRRSS--   -
               SCOP domains d3h5oa_ A: automated matches                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhh....eeeee......hhhhhhhhh...eeeee........eee.hhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhh...hhh.eeee....hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhh........eee....hhhhh.......eee.hhhhhhhhhhhhhhhhhh.......eee...eee.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h5o A  71 RTVLVLIPSLANTVFLETLTGIETVLDAAGYQmLIGNSHYDAGQELQLLRAYLQHRPDGVLITGLSHAEPFERILSQHALPVVYmmDLADDGRCCVGFSQEDAGAAITRHLLSRGKRRIGFLGAQLDERVmKRLDGYRAALDAADCRDAGLEWLDPQPSSmQmGADmLDRALAERPDCDALFCCNDDLAIGALARSQQLGIAVPERLAIAGFNDLQPAAWCTPPLTTVATPRRDIGVHAAKALLQLIDGEEPASRRADLGFRLmLRRSSEG 341
                                    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 
                                                          103-MSE                                             155-MSE                                       201-MSE                       231-MSE |                                                                                              334-MSE   
                                                                                                               156-MSE                                                                      233-MSE                                                                                                        
                                                                                                                                                                                                237-MSE                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:271
 aligned with Q7NTU7_CHRVO | Q7NTU7 from UniProtKB/TrEMBL  Length:339

    Alignment length:271
                                                                                                                                                                                                                                                                                                      339  
                                    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        |- 
         Q7NTU7_CHRVO    71 RTVLVLIPSLANTVFLETLTGIETVLDAAGYQMLIGNSHYDAGQELQLLRAYLQHRPDGVLITGLSHAEPFERILSQHALPVVYMMDLADDGRCCVGFSQEDAGAAITRHLLSRGKRRIGFLGAQLDERVMKRLDGYRAALDAADCRDAGLEWLDPQPSSMQMGADMLDRALAERPDCDALFCCNDDLAIGALARSQQLGIAVPERLAIAGFNDLQPAAWCTPPLTTVATPRRDIGVHAAKALLQLIDGEEPASRRADLGFRLMLRRSS--   -
               SCOP domains d3h5ob_ B: automated matches                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhh....eeeee......hhhhhhhhh...eeeee........eee.hhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhhh..hhh.eeee....hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhh........eee....hhhhh.......eee.hhhhhhhhhhhhhhhhhh.......eee...eee.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h5o B  71 RTVLVLIPSLANTVFLETLTGIETVLDAAGYQmLIGNSHYDAGQELQLLRAYLQHRPDGVLITGLSHAEPFERILSQHALPVVYmmDLADDGRCCVGFSQEDAGAAITRHLLSRGKRRIGFLGAQLDERVmKRLDGYRAALDAADCRDAGLEWLDPQPSSmQmGADmLDRALAERPDCDALFCCNDDLAIGALARSQQLGIAVPERLAIAGFNDLQPAAWCTPPLTTVATPRRDIGVHAAKALLQLIDGEEPASRRADLGFRLmLRRSSEG 341
                                    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 
                                                          103-MSE                                             155-MSE                                       201-MSE                       231-MSE |                                                                                              334-MSE   
                                                                                                               156-MSE                                                                      233-MSE                                                                                                        
                                                                                                                                                                                                237-MSE
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H5O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H5O)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q7NTU7_CHRVO | Q7NTU7)
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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