Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  SINR, MASTER REGULATOR OF BIOFILM FORMATION IN BACILLUS SUBTILIS
 
Authors :  V. L. Colledge, M. J. Fogg, V. M. Levdikov, A. Leech, E. J. Dodson, A. J. Wi
Date :  23 Feb 11  (Deposition) - 08 Jun 11  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription, Transcription Regulator, Antagonist, Sporulation (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 Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Fragment: OLIGOMERISATION DOMAIN, RESIDUES 75-111
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Other Details: GPA TAG AT N-TERMINUS, NI BOUND BETWEEN N-TERMINI OF A CHAIN AND SYMMETRY EQUIVALENT OF THE B CHAIN
    Strain: 168
    Synonym: SINR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NI1Ligand/IonNICKEL (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:71 , PRO A:72 , GLY B:71 , PRO B:72BINDING SITE FOR RESIDUE NI A1110

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:71 -Pro A:72
2Gly B:71 -Pro B:72

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SINPS51500 Sin domain profile.SINR_BACSU65-103
 		  2A:75-103
B:75-103

(-) Exons   (0, 0)

(no "Exon" information available for 2YAL)

(-) 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:39
 aligned with SINR_BACSU | P06533 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:69
                                    50        60        70        80        90       100         
           SINR_BACSU    41 NPSIQFLEKVSAVLDVSVHTLLDEKHETEYDGQLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQK 109
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....------------------------------hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------SIN  PDB: A:75-103 UniProt: 65-103     ------ PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 2yal A  71 GPAI------------------------------DSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQK 109
                               |     -         -         -    |   80        90       100         
                              74                             75                                  


Chain B from PDB  Type:PROTEIN  Length:38
 aligned with SINR_BACSU | P06533 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:68
                                    50        60        70        80        90       100        
           SINR_BACSU    41 NPSIQFLEKVSAVLDVSVHTLLDEKHETEYDGQLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ 108
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------SinI-2yalB01 B:75-103        ----- Pfam domains (1)
           Pfam domains (2) ----------------------------------SinI-2yalB02 B:75-103        ----- Pfam domains (2)
         Sec.struct. author ....------------------------------.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------SIN  PDB: B:75-103 UniProt: 65-103     ----- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 2yal B  71 GPAI------------------------------DSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ 108
                               |     -         -         -    |   80        90       100        
                              74                             75
   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 2YAL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YAL)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: SinI] (1)
(-)
Family: SinI (1)
(-)
Bacillus subtilis (1)
1aSinI-2yalB01B:75-103
1bSinI-2yalB02B:75-103

(-) Gene Ontology  (7, 7)

Asymmetric/Biological 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/Biological 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
    NI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:71 - Pro A:72   [ RasMol ]  
    Gly B:71 - Pro B:72   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  2yal
    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 3qq6 3zkc

(-) Related Entries Specified in the PDB File

1b0n SINR PROTEIN/SINI PROTEIN COMPLEX