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 :  CRYSTAL STRUCTURE OF TETR TRANSCRIPTIONAL REGULATOR FROM AGROBACTERIUM TUMEFACIENS
 
Authors :  J. Osipiuk, T. Skarina, H. Zheng, A. Savchenko, A. M. Edwards, A. Joachi Midwest Center For Structural Genomics (Mcsg)
Date :  24 Jan 08  (Deposition) - 05 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Apc5923, Tetr, Transcription, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Osipiuk, T. Skarina, H. Zheng, A. Savchenko, A. M. Edwards, A. Joachimiak
X-Ray Crystal Structure Of Tetr Transcriptional Regulator From Agrobacterium Tumefaciens.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR, TETR FAMILY
    Atcc33970
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidMODIFIED PET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneATU2020, AGR_C_3662
    Organism ScientificAGROBACTERIUM TUMEFACIENS STR.
    Organism Taxid176299
    StrainC58

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:134 , ARG A:164BINDING SITE FOR RESIDUE FMT A 302
2AC2SOFTWAREASP A:173 , ARG B:134 , GLU B:160 , ARG B:164BINDING SITE FOR RESIDUE FMT B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C2B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C2B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C2B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C2B)

(-) Exons   (0, 0)

(no "Exon" information available for 3C2B)

(-) 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:200
 aligned with A9CID8_AGRFC | A9CID8 from UniProtKB/TrEMBL  Length:217

    Alignment length:203
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
         A9CID8_AGRFC    12 SPRQNAVLDQALRLLVEGGEKALTTSGLARAANCSKESLYKWFGDRDGLLAAMITFQQSKVRTFEKAGDRVSAPQLADHLEVFAHDLLDVLAGDVSLALNRLAIGQASRDGSKLGDLLLERGRRQIDRRARGLIEAGRRSGYLRFDDAEEAYRSFYGLIVSDLHVRMLLGEAPDKDFSARAKKAVVAFLTLYGTEKVHSELGG 214
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c2bA01 A:12-63 Homeodomain-like                    -3c2bA02 A:65-214 Tetracycline Repressor, domain 2                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.---hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c2b A  12 SPRQNAVLDQALRLLVEGGEKALTTSGLARAANCSKESLYKWFGDRDGLLAAmITFQQSKVRTFEKAGDRVSAPQLADHLEVFAHDLLDVLAGDVSLALNRLAIGQASR---KLGDLLLERGRRQIDRRARGLIEAGRRSGYLRFDDAEEAYRSFYGLIVSDLHVRmLLGEAPDKDFSARAKKAVVAFLTLYGTEKVHSELGG 214
                                    21        31        41        51        61  |     71        81        91       101       111        |-  |    131       141       151       161       171      |181       191       201       211   
                                                                               64-MSE                                                 120 124                                                   178-MSE                                

Chain B from PDB  Type:PROTEIN  Length:194
 aligned with A9CID8_AGRFC | A9CID8 from UniProtKB/TrEMBL  Length:217

    Alignment length:202
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
         A9CID8_AGRFC    11 FSPRQNAVLDQALRLLVEGGEKALTTSGLARAANCSKESLYKWFGDRDGLLAAMITFQQSKVRTFEKAGDRVSAPQLADHLEVFAHDLLDVLAGDVSLALNRLAIGQASRDGSKLGDLLLERGRRQIDRRARGLIEAGRRSGYLRFDDAEEAYRSFYGLIVSDLHVRMLLGEAPDKDFSARAKKAVVAFLTLYGTEKVHSEL 212
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c2bB01 B:11-60 Homeodomain-like                  3c2bB02 B:61       -212 Tetracycline Repressor, domain 2                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhh.-------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.....-hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c2b B  11 FSPRQNAVLDQALRLLVEGGEKALTTSGLARAANCSKESLYKWFGDRDGLLAAmITFQQSKV-------DRVSAPQLADHLEVFAHDLLDVLAGDVSLALNRLAIGQASRDGSKLGDLLLERGRRQIDRRARGLIEAGRRSGYLRFDDAEEAYRSFYGLIVSDLHVRmLLGEAPD-DFSARAKKAVVAFLTLYGTEKVHSEL 212
                                    20        30        40        50        60   |    70 |      80        90       100       110       120       130       140       150       160       170       180    | |190       200       210  
                                                                                64-MSE  72      80                                                                                               178-MSE185 |                         
                                                                                                                                                                                                          187                         

   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 3C2B)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C2B)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A9CID8_AGRFC | A9CID8)
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
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3c2b)
 

(-) 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
  3c2b
    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
  A9CID8_AGRFC | A9CID8
    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
  A9CID8_AGRFC | A9CID8
    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 3C2B)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3C2B)