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(-) Description

Title :  CRYSTAL STRUCTURE OF PERIPLASMIC BINDING RIBOSE OPERON REPRESSOR PROTEIN FROM LACTOBACILLUS ACIDOPHILUS
 
Authors :  R. Agarwal, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  10 Jun 09  (Deposition) - 23 Jun 09  (Release) - 23 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Crystal Structure, Psi-Ii, Nysgxrc, 11235H, Periplasmic Binding Protein, Ribose Operon Repressor, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Dna-Binding, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Agarwal, S. K. Burley, S. Swaminathan
Crystal Structure Of Periplasmic Binding Ribose Operon Repressor Protein From Lactobacillus Acidophilus
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSE OPERON REPRESSOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSGX3(BC)
    Expression System Strain: BL21 (DE3)RIPL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RBSR, LBA1472
    Organism Scientific: LACTOBACILLUS ACIDOPHILUS
    Organism Taxid: 1579
    Strain: NCFM

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3HS3)

(-) Sites  (0, 0)

(no "Site" information available for 3HS3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HS3)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ile A:253 -Pro A:254
2Ser A:272 -Pro A:273
3Ile B:253 -Pro B:254
4Ser B:272 -Pro B:273

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HS3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HS3)

(-) Exons   (0, 0)

(no "Exon" information available for 3HS3)

(-) Sequences/Alignments

Asymmetric/Biological 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:264
 aligned with Q5FJ32_LACAC | Q5FJ32 from UniProtKB/TrEMBL  Length:319

    Alignment length:264
                                                                                                                                                                                                                                                                                                319 
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316  | 
         Q5FJ32_LACAC    57 KKSKMIGIIIPDLNNRFYAQIIDGIQEVIQKEGYTALISFSTNSDVKKYQNAIINFENNNVDGIITSAFTIPPNFHLNTPLVMYDSANINDDIVRIVSNNTKGGKESIKLLSKKIEKVLIQHWPLSLPTIRERIEAMTAEASKLKIDYLLEETPENNPYISAQSALNKSNQFDAIITVNDLYAAEIIKEAKRRNLKIPDDFQLVGYDNNILCGYTSPTISTIDQNPKLIGQTAAHRLLDLMSGNNSTRNSIIDVLPIKRDSTL-   -
               SCOP domains d3hs3a_ A: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhh...eeeee.............eeee.........eeeeehhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh.eee..hhhhhhhhhhhhhhh........eee....hhhhhh......eee.hhhhhhhhhhhhhhhhh........eee..eee.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hs3 A  57 KKSKMIGIIIPDLNNRFYAQIIDGIQEVIQKEGYTALISFSTNSDVKKYQNAIINFENNNVDGIITSAFTIPPNFHLNTPLVMYDSANINDDIVRIVSNNTKGGKESIKLLSKKIEKVLIQHWPLSLPTIRERIEAMTAEASKLKIDYLLEETPENNPYISAQSALNKSNQFDAIITVNDLYAAEIIKEAKRRNLKIPDDFQLVGYDNNILCGYTSPTISTIDQNPKLIGQTAAHRLLDLMSGNNSTRNSIIDVLPIKRDSTEG 320
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316    


Chain B from PDB  Type:PROTEIN  Length:264
 aligned with Q5FJ32_LACAC | Q5FJ32 from UniProtKB/TrEMBL  Length:319

    Alignment length:264
                                                                                                                                                                                                                                                                                                319 
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316  | 
         Q5FJ32_LACAC    57 KKSKMIGIIIPDLNNRFYAQIIDGIQEVIQKEGYTALISFSTNSDVKKYQNAIINFENNNVDGIITSAFTIPPNFHLNTPLVMYDSANINDDIVRIVSNNTKGGKESIKLLSKKIEKVLIQHWPLSLPTIRERIEAMTAEASKLKIDYLLEETPENNPYISAQSALNKSNQFDAIITVNDLYAAEIIKEAKRRNLKIPDDFQLVGYDNNILCGYTSPTISTIDQNPKLIGQTAAHRLLDLMSGNNSTRNSIIDVLPIKRDSTL-   -
               SCOP domains d3hs3b_ B: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhh...eeeee.............eeee.........eeeeehhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh.eee..hhhhhhhhhhhhhhh........eee....hhhhhh......eee.hhhhhhhhhhhhhhhhh........eee..eee.hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hs3 B  57 KKSKMIGIIIPDLNNRFYAQIIDGIQEVIQKEGYTALISFSTNSDVKKYQNAIINFENNNVDGIITSAFTIPPNFHLNTPLVMYDSANINDDIVRIVSNNTKGGKESIKLLSKKIEKVLIQHWPLSLPTIRERIEAMTAEASKLKIDYLLEETPENNPYISAQSALNKSNQFDAIITVNDLYAAEIIKEAKRRNLKIPDDFQLVGYDNNILCGYTSPTISTIDQNPKLIGQTAAHRLLDLMSGNNSTRNSIIDVLPIKRDSTEG 320
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HS3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HS3)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5FJ32_LACAC | Q5FJ32)
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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  Cis Peptide Bonds
    Ile A:253 - Pro A:254   [ RasMol ]  
    Ile B:253 - Pro B:254   [ RasMol ]  
    Ser A:272 - Pro A:273   [ RasMol ]  
    Ser B:272 - Pro B:273   [ RasMol ]  
 

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