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 THE TETR TRANSCRIPTION REGULATORY PROTEIN FROM MYCOBACTERIUM VANBAALENII
 
Authors :  J. B. Bonanno, J. Freeman, K. T. Bain, J. Adams, R. Romero, D. Smith, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  10 Aug 07  (Deposition) - 28 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Transcription, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Dna-Binding, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. B. Bonanno, J. Freeman, K. T. Bain, J. Adams, R. Romero, D. Smith, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of The Tetr Transcription Regulatory Protein From Mycobacterium Vanbaalenii.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR, TETR FAMILY
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidMODIFIED PET26
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET
    Expression System Vector TypePLASMID
    GeneTETR, MVAN_0763
    MutationYES
    Organism ScientificMYCOBACTERIUM VANBAALENII PYR-1
    Organism Taxid350058
    StrainPYR-1, DSM 7251

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2QWT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QWT)

(-) 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:167
 aligned with A1T351_MYCVP | A1T351 from UniProtKB/TrEMBL  Length:186

    Alignment length:179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173         
         A1T351_MYCVP     4 PLRADAARNRARVLEVAYDTFAAEGLGVPIDEIARRAGVGAGTVYRHFPTKQALVVAVAEDRVRRIVDHARTLLAAEGPGEALFVFLRDMVRSAAADYGLVDALVGYGLDLEVAAPGAEAAFLATLGELLAAAQRAGTVRADVDVAVIKALLVVCKVPQVYDGEVSERVVRVIEDGLRV 182
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qwtA00 A:4-182 Tetracycline Repressor, domain 2                                                                                                                                    CATH domains
               Pfam domains ------------TetR_N-2qwtA01 A:16-61                        ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh------------hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qwt A   4 PLRADAARNRARVLEVAYDTFAAEGLGVPMDEIARRAGVGAGTVYRHFPTKQALVVAVAEDRVRRIVDHARTLLAAEGPGEALFVFMRDMVRSAAADYGLVDALVGYGLDLEVAAPGAEAAFLATLGELLAAAQRAGTVRADVDVAVIKALL------------VSERVVRVIEDGLRV 182
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153 |       -    |  173         
                                                                                                                                                                                 155          168              

   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 2QWT)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A1T351_MYCVP | A1T351)
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/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
(no "Ligands, Modified Residues, Ions" information available for 2qwt)
 
  Sites
(no "Sites" information available for 2qwt)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2qwt)
 

(-) 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
  2qwt
    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
  A1T351_MYCVP | A1T351
    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
  A1T351_MYCVP | A1T351
    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 2QWT)

(-) Related Entries Specified in the PDB File

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