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

(-) Description

Title :  CRYSTAL STRUCTURE OF A TETR/ACRR FAMILY TRANSCRIPTIONAL REGULATOR FROM RHODOCOCCUS SP. RHA1
 
Authors :  R. Zhang, T. Skarina, O. Kagan, A. Savchenko, A. M. Edwards, A. Joachimi Midwest Center For Structural Genomics (Mcsg)
Date :  14 Sep 07  (Deposition) - 25 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tetr/Acrr Family Transcriptional Regulator, Structural Genomics, Psi- 2, Rha08332, Mcsg, Protein Structure Initiative, Midwest Center For Structural Genomics, Dna-Binding, Transcription Regulation, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Zhang, T. Skarina, O. Kagan, A. Savchenko, A. M. Edwards, A. Joachimiak
The Crystal Structure Of A Tetr/Acrr Family Transcriptional Regulator From Rhodococcus Sp. Rha1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR, ACRR FAMILY PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPDM68
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneRHA08332, RHA1_RO06070
    Organism ScientificRHODOCOCCUS SP.
    Organism Taxid101510
    StrainRHA1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2RAE)

(-) Sites  (0, 0)

(no "Site" information available for 2RAE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RAE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RAE)

(-) Exons   (0, 0)

(no "Exon" information available for 2RAE)

(-) 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:193
 aligned with Q0S3N9_RHOJR | Q0S3N9 from UniProtKB/TrEMBL  Length:207

    Alignment length:193
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   
         Q0S3N9_RHOJR    11 IGRRPSTTQDRISTVGIELFTEQGFDATSVDEVAEASGIARRTLFRYFPSKNAIPWGDFDAHLAEMRAQLAAQPDDIPIVDGLTAALLQFNAFPASEEINHRKRMGLILRVPALQAYSVVMYEGWRNVIAEYVASRLGTSPTDHVPRTVGYLLLGVAMSAYEQWLDDDSLELNELLASGMQSLYDGLSSLGEP 203
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------2raeA01 A:17-59 Homeodomain-like           2raeA02 A:60-196 Tetracycline Repressor, domain 2                                                                                        ------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rae A  11 IGRRPSTTQDRISTVGIELFTEQGFDATSVDEVAEASGIARRTLFRYFPSKNAIPWGDFDAHLAEMRAQLAAQPDDIPIVDGLTAALLQFNAFPASEEINHRKRMGLILRVPALQAYSVVMYEGWRNVIAEYVASRLGTSPTDHVPRTVGYLLLGVAMSAYEQWLDDDSLELNELLASGMQSLYDGLSSLGEP 203
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   

   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 2RAE)

(-) CATH Domains  (2, 2)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2RAE)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q0S3N9_RHOJR | Q0S3N9)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
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 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 2rae)
 
  Sites
(no "Sites" information available for 2rae)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2rae)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2rae
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q0S3N9_RHOJR | Q0S3N9
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q0S3N9_RHOJR | Q0S3N9
    Protein Disorder PredictionDisEMBL | 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 2RAE)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2RAE)