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

(-) Description

Title :  TM1030 CRYSTALLIZED AT 323K
 
Authors :  K. D. Koclega, M. Chruszcz, G. Bujacz, A. Joachimiak, W. Minor, Midwest For Structural Genomics (Mcsg)
Date :  29 Jul 09  (Deposition) - 11 Aug 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tm1030, Transcriptional Regulator, Temperature, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Dna-Binding, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. D. Koclega, M. Chruszcz, M. D. Zimmerman, G. Bujacz, W. Minor
'Hot' Macromolecular Crystals.
Cryst. Growth Des. V. 10 580 2010
PubMed-ID: 20161694  |  Reference-DOI: 10.1021/CG900971H

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR, TETR FAMILY
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: B834(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM1030, TM_1030
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3IH2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IH2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IH2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IH2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IH2)

(-) Exons   (0, 0)

(no "Exon" information available for 3IH2)

(-) 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:201
 aligned with Q9X0C0_THEMA | Q9X0C0 from UniProtKB/TrEMBL  Length:200

    Alignment length:201
                             1                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199 
         Q9X0C0_THEMA     - -MLSKRDAILKAAVEVFGKKGYDRATTDEIAEKAGVAKGLIFHYFKNKEELYYQAYMSVTEKLQKEFENFLMKNRNRDIFDFMERWIEKKLEYSASHPEEADFLITLVSVDEGLRKRILLDLEKSQRVFFDFVREKLKDLDLAEDVTEEIALKFLMWFFSGFEEVYLRTYQGKPELLKRDMNTLVEEVKVMLRILKKGMTK 200
               SCOP domains d3ih2a1 A:0-75 Transcriptional regulator TM1030                             d3ih2a2 A:76-200 Transcriptional regulator TM1030                                                                             SCOP domains
               CATH domains 3ih2A01 A:0-46 Homeodomain-like                3ih2A02 A:47-200 Tetracycline Repressor, domain 2                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ih2 A   0 HmLSKRDAILKAAVEVFGKKGYDRATTDEIAEKAGVAKGLIFHYFKNKEELYYQAYmSVTEKLQKEFENFLmKNRNRDIFDFmERWIEKKLEYSASHPEEADFLITLVSVDEGLRKRILLDLEKSQRVFFDFVREKLKDLDLAEDVTEEIALKFLmWFFSGFEEVYLRTYQGKPELLKRDmNTLVEEVKVmLRILKKGmTK 200
                             |       9        19        29        39        49      | 59        69 |      79  |     89        99       109       119       129       139       149     | 159       169       179|      189|      199 
                             |                                                     56-MSE         71-MSE     82-MSE                                                                  155-MSE                  180-MSE   190-MSE 198-MSE
                             1-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  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IH2)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9X0C0_THEMA | Q9X0C0)
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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3ih2)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ih2)
 
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
[ Asym. Unit PNG format | Biol. Unit 1 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
  3ih2
    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
  Q9X0C0_THEMA | Q9X0C0
    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
  Q9X0C0_THEMA | Q9X0C0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9X0C0_THEMA | Q9X0C0: 1z77 1zkg 2id6 2iek 3ih3 3ih4 4i6z 4i76

(-) Related Entries Specified in the PDB File

3ih3 3ih4