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
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE SENSOR DOMAIN OF THE TRANSCRIPTIONAL REGULATOR DNR FROM PSEUDOMONAS AERUGINOSA
 
Authors :  G. Giardina, K. A. Johnson, A. Di Matteo
Date :  24 Jul 07  (Deposition) - 18 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Beta Barrel, Dimerization Helix, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Giardina, S. Rinaldo, K. A. Johnson, A. Di Matteo, M. Brunori, F. Cutruzzola
No Sensing In Pseudomonas Aeruginosa: Structure Of The Transcriptional Regulator Dnr.
J. Mol. Biol. V. 378 1002 2008
PubMed-ID: 18420222  |  Reference-DOI: 10.1016/J.JMB.2008.03.013

(-) Compounds

Molecule 1 - DNR PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Fragment: SENSOR DOMAIN
    Gene: DNR
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Strain: PAO1
    Synonym: TRANSCRIPTIONAL REGULATOR DNR, DNR DISSIMILATIVE NITRATE RESPIRATION REGULATOR

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2Z69)

(-) Sites  (0, 0)

(no "Site" information available for 2Z69)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z69)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z69)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z69)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z69)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z69)

(-) 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:148
 aligned with Q51441_PSEAI | Q51441 from UniProtKB/TrEMBL  Length:227

    Alignment length:153
                               1                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147   
         Q51441_PSEAI     - ---MEFQRVHQQLLQSHHLFEPLSPVQLQELLASSDLVNLDKGAYVFRQGEPAHAFYYLISGCVKIYRLTPEGQEKILEVTNERNTFAEAMMFMDTPNYVATAQAVVPSQLFRFSNKAYLRQLQDNTPLALALLAKLSTRLHQRIDEIETLSL 150
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh........hhhhhhhhhhh.eeeee....eee.......eeeeeee..eeee....-----..eee...eeehhhhhhh.......eeee...eeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z69 A  -2 GSHMEFQRVHQQLLQSHHLFEPLSPVQLQELLASSDLVNLDKGAYVFRQGEPAHAFYYLISGCVKIYRLTP-----ILEVTNERNTFAEAMMFMDTPNYVATAQAVVPSQLFRFSNKAYLRQLQDNTPLALALLAKLSTRLHQRIDEIETLSL 150
                                     7        17        27        37        47        57        67|     | 77        87        97       107       117       127       137       147   
                                                                                                 68    74                                                                            


Chain B from PDB  Type:PROTEIN  Length:150
 aligned with Q51441_PSEAI | Q51441 from UniProtKB/TrEMBL  Length:227

    Alignment length:150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
         Q51441_PSEAI     1 MEFQRVHQQLLQSHHLFEPLSPVQLQELLASSDLVNLDKGAYVFRQGEPAHAFYYLISGCVKIYRLTPEGQEKILEVTNERNTFAEAMMFMDTPNYVATAQAVVPSQLFRFSNKAYLRQLQDNTPLALALLAKLSTRLHQRIDEIETLSL 150
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh........hhhhhhhhhhh.eeeee....eee.......eeeeeee.eeeeeee.....eeeeeeee...eehhhhhhh.......eeee...eeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z69 B   1 MEFQRVHQQLLQSHHLFEPLSPVQLQELLASSDLVNLDKGAYVFRQGEPAHAFYYLISGCVKIYRLTPEGQEKILEVTNERNTFAEAMMFMDTPNYVATAQAVVPSQLFRFSNKAYLRQLQDNTPLALALLAKLSTRLHQRIDEIETLSL 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150


Chain C from PDB  Type:PROTEIN  Length:138
 aligned with Q51441_PSEAI | Q51441 from UniProtKB/TrEMBL  Length:227

    Alignment length:144
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146    
         Q51441_PSEAI     7 HQQLLQSHHLFEPLSPVQLQELLASSDLVNLDKGAYVFRQGEPAHAFYYLISGCVKIYRLTPEGQEKILEVTNERNTFAEAMMFMDTPNYVATAQAVVPSQLFRFSNKAYLRQLQDNTPLALALLAKLSTRLHQRIDEIETLSL 150
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............hhhhhhhhhh..eeeee....eee.......eeeeeeeeeeeeee.----..eeeeee...eeehhhhhhh.......eeeeeeeeeeeeeehhhhhhhhh.hhhhhhhhhhhhh......--....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z69 C   7 HQQLLQSHHLFEPLSPVQLQELLASSDLVNLDKGAYVFRQGEPAHAFYYLISGCVKIYRL----QEKILEVTNERNTFAEAMMFMDTPNYVATAQAVVPSQLFRFSNKAYLRQLQDNTPLALALLAKLSTRLHQR--EIETLSL 150
                                    16        26        36        46        56        66    |   76        86        96       106       116       126       136    |  146    
                                                                                      66   71                                                                   141  |      
                                                                                                                                                                   144
   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 2Z69)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z69)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Z69)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q51441_PSEAI | Q51441)
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:0051173    positive regulation of nitrogen compound metabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
    GO:0051353    positive regulation of oxidoreductase activity    Any process that activates or increases the frequency, rate or extent of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0071731    response to nitric oxide    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus.
    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 2z69)
 
  Sites
(no "Sites" information available for 2z69)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2z69)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  2z69
    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
  Q51441_PSEAI | Q51441
    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
  Q51441_PSEAI | Q51441
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q51441_PSEAI | Q51441: 3dkw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2Z69)