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

(-) Description

Title :  CRYSTAL STRUCTURE OF MARR FAMILY TRANSCRIPTIONAL REGULATOR FROM SILICIBACTER POMEROYI
 
Authors :  C. Chang, L. Volkart, L. Freeman, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  17 Dec 07  (Deposition) - 01 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Silicibacter Pomeroyi, Transcriptional Regulator, Marr Family, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Dna-Binding, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, L. Volkart, L. Freeman, A. Joachimiak
Crystal Structure Of Marr Family Transcriptional Regulator.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR, MARR FAMILY
    Atcc: 700808
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG
    Expression System Strain: BL21(DE3) DERIVATIVE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SPOA0452
    Organism Scientific: SILICIBACTER POMEROYI DSS-3
    Organism Taxid: 246200
    Strain: DSS-3, DSM 15171

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3BOQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BOQ)

(-) 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:136
 aligned with Q5LLB8_RUEPO | Q5LLB8 from UniProtKB/TrEMBL  Length:157

    Alignment length:144
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146    
         Q5LLB8_RUEPO     7 KSDRQQNQTRLWLNILRLHGLVFGDLNRQLLDETGLSLAKFDAMAQLARNPDGLSMGKLSGALKVTNGNVSGLVNRLIKDGMVVKAMSADDRRSFSAKLTDAGLTTFKQASEAHNRILAELLRAVSDQDMVEASAALRGILESM 150
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3boqA00 A:7-149 'winged helix' repressor DNA binding domain                                                                                    - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...eehhhhhhhh.....hhhhhhhhhhhh..eee.--------.eeeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3boq A   7 KSDRQQNQTRLWLNILRLHGLVFGDLNRQLLDETGLSLAKFDAmAQLARNPDGLSmGKLSGALKVTNGNVSGLVNRLIKDGmVVKA--------FSAKLTDAGLTTFKQASEAHNRILAELLRAVSDQDmVEASAALRGILESm 150
                                    16        26        36        46   |    56     |  66        76        86 |   |   -    |  106       116       126       136       146   |
                                                                      50-MSE      62-MSE                    88-MSE      101                                136-MSE       150-MSE


Chain B from PDB  Type:PROTEIN  Length:138
 aligned with Q5LLB8_RUEPO | Q5LLB8 from UniProtKB/TrEMBL  Length:157

    Alignment length:145
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146     
         Q5LLB8_RUEPO     7 KSDRQQNQTRLWLNILRLHGLVFGDLNRQLLDETGLSLAKFDAMAQLARNPDGLSMGKLSGALKVTNGNVSGLVNRLIKDGMVVKAMSADDRRSFSAKLTDAGLTTFKQASEAHNRILAELLRAVSDQDMVEASAALRGILESMQ 151
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3boqB00 B:7-151 'winged helix' repressor DNA binding domain                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...eehhhhhhhh.....hhhhhhhhhhhh......-------..ee..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3boq B   7 KSDRQQNQTRLWLNILRLHGLVFGDLNRQLLDETGLSLAKFDAmAQLARNPDGLSmGKLSGALKVTNGNVSGLVNRLIKDGmVVKA-------SFSAKLTDAGLTTFKQASEAHNRILAELLRAVSDQDmVEASAALRGILESmQ 151
                                    16        26        36        46   |    56     |  66        76        86 |   |   -   |   106       116       126       136       146   | 
                                                                      50-MSE      62-MSE                    88-MSE     100                                 136-MSE       150-MSE
   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 3BOQ)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5LLB8_RUEPO | Q5LLB8)
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.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3boq)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3boq)
 

(-) 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 ](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
  3boq
    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
  Q5LLB8_RUEPO | Q5LLB8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q5LLB8_RUEPO | Q5LLB8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3BOQ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3BOQ)