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 :  THE CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR PA3006
 
Authors :  V. V. Lunin, T. Skarina, O. Onopriyenko, Y. Kim, A. Joachimiak, A. M. Edw A. Savchenko, Midwest Center For Structural Genomics (Mcsg)
Date :  09 Dec 05  (Deposition) - 20 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Pa3006, Apc5893, Transcriptional Regulator, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. V. Lunin, T. Skarina, O. Onopriyenko, Y. Kim, A. Joachimiak, A. M. Edwards, A. Savchenko
The Crystal Structure Of Transcriptional Regulator Pa3006
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE TRANSCRIPTIONAL REGULATOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: MODIFIED PET15B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 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 2FBQ)

(-) Sites  (0, 0)

(no "Site" information available for 2FBQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2FBQ)

(-) 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:213
 aligned with Q9HZJ9_PSEAE | Q9HZJ9 from UniProtKB/TrEMBL  Length:233

    Alignment length:213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
         Q9HZJ9_PSEAE     2 AQSETVERILDAAEQLFAEKGFAETSLRLITSKAGVNLAAVNYHFGSKKALIQAVFSRFLGPFCASLEKELDRRQAKPEAQHATLEDLLHLLVSQAMAVKPRSGNDLSIFMRLLGLAFSQSQGHLRKYLEEVYGKVFRRYMLLVNEAAPKLPPIELFWRVHFMLGAAAFSMSGIKALRAMAETDFGVNTSTEQVMHLMVPFFAAGMRAESGID 214
               SCOP domains d2fbqa1 A:2-80 Transcriptional regulator PsrA                                  d2fbqa2 A:81-214 Transcriptional regulator PsrA                                                                                        SCOP domains
               CATH domains 2fbqA00 A:2-214 Tetracycline Repressor, domain 2                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fbq A   2 AQSETVERILDAAEQLFAEKGFAETSLRLITSKAGVNLAAVNYHFGSKKALIQAVFSRFLGPFCASLEKELDRRQAKPEAQHATLEDLLHLLVSQAMAVKPRSGNDLSIFMRLLGLAFSQSQGHLRKYLEEVYGKVFRRYMLLVNEAAPKLPPIELFWRVHFMLGAAAFSMSGIKALRAMAETDFGVNTSTEQVMHLMVPFFAAGMRAESGID 214
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9HZJ9_PSEAE | Q9HZJ9)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
    GO:0050714    positive regulation of protein secretion    Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    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 2fbq)
 
  Sites
(no "Sites" information available for 2fbq)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2fbq)
 
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
  2fbq
    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
  Q9HZJ9_PSEAE | Q9HZJ9
    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
  Q9HZJ9_PSEAE | Q9HZJ9
    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 2FBQ)

(-) Related Entries Specified in the PDB File

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