Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  THE N-TERMINAL DNA BINDING DOMAIN OF SINR FROM BACILLUS SUBTILIS
 
Authors :  V. Colledge, M. J. Fogg, V. M. Levdikov, E. J. Dodson, A. J. Wilkinson
Date :  15 Feb 11  (Deposition) - 15 Jun 11  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Helix-Turn-Helix Motif, Biofilm, Repressor, Transcriptional Regulator, Sini, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. L. Colledge, M. J. Fogg, V. M. Levdikov, A. Leech, E. J. Dodson, A. J. Wilkinson
Structure And Organisation Of Sinr, The Master Regulator Of Biofilm Formation In Bacillus Subtilis.
J. Mol. Biol. V. 411 597 2011
PubMed-ID: 21708175  |  Reference-DOI: 10.1016/J.JMB.2011.06.004

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR SINR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-YSBLIC-
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN OF SINR RESIDUES 1-69
    Gene: BSU24610, FLAD, SIN, SINR
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3QQ6)

(-) Sites  (0, 0)

(no "Site" information available for 3QQ6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QQ6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QQ6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QQ6)

(-) PROSITE Motifs  (2, 3)

Asymmetric Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_CROC1PS50943 Cro/C1-type HTH domain profile.SINR_BACSU6-61
 		  2A:6-61
B:6-61
2SINPS51500 Sin domain profile.SINR_BACSU65-103  1A:65-67
Biological Unit 1 (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_CROC1PS50943 Cro/C1-type HTH domain profile.SINR_BACSU6-61
 		  2A:6-61
B:6-61
2SINPS51500 Sin domain profile.SINR_BACSU65-103  1A:65-67
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_CROC1PS50943 Cro/C1-type HTH domain profile.SINR_BACSU6-61
 		  1A:6-61
-
2SINPS51500 Sin domain profile.SINR_BACSU65-103  1A:65-67
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_CROC1PS50943 Cro/C1-type HTH domain profile.SINR_BACSU6-61
 		  1-
B:6-61
2SINPS51500 Sin domain profile.SINR_BACSU65-103  0-

(-) Exons   (0, 0)

(no "Exon" information available for 3QQ6)

(-) 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:69
 aligned with SINR_BACSU | P06533 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:69
                              1                                                                  
                              |      8        18        28        38        48        58         
            SINR_BACSU    - --MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHTLLDEKHE 67
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------HTH_CROC1  PDB: A:6-61 UniProt: 6-61                    ---SIN PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  3qq6 A -1 HHMIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHTLLDEKHE 67
                                     8        18        28        38        48        58         


Chain B from PDB  Type:PROTEIN  Length:68
 aligned with SINR_BACSU | P06533 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:68
                                1                                                               
                                |    6        16        26        36        46        56        
            SINR_BACSU    - ----MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHTLLDE 64
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------HTH_3-3qq6B01 B:6-61                                    --- Pfam domains (1)
           Pfam domains (2) ---------HTH_3-3qq6B02 B:6-61                                    --- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------HTH_CROC1  PDB: B:6-61 UniProt: 6-61                    --- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  3qq6 B -3 HHHHMIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHTLLDE 64
                                     6        16        26        36        46        56
   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  (0, 0)

(no "SCOP Domain" information available for 3QQ6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QQ6)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SINR_BACSU | P06533)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3qq6)
 
  Sites
(no "Sites" information available for 3qq6)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3qq6)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3qq6
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SINR_BACSU | P06533
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SINR_BACSU | P06533
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SINR_BACSU | P06533: 1b0n 2yal 3zkc

(-) Related Entries Specified in the PDB File

1b0n SINR/SINI PROTEIN COMPLEX