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 :  STRUCTURE OF THE CRO PROTEIN FROM PROPHAGE PFL 6 IN PSEUDOMONAS FLUORESCENS PF-5
 
Authors :  C. G. Roessler, S. A. Roberts, W. R. Montfort, M. H. J. Cordes
Date :  13 Apr 07  (Deposition) - 04 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription Factor, Helix-Turn-Helix, Prophage, Structural Evolution, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. G. Roessler, B. M. Hall, W. J. Anderson, W. M. Ingram, S. A. Roberts, W. R. Montfort, M. H. Cordes
Transitive Homology-Guided Structural Studies Lead To Discovery Of Cro Proteins With 40% Sequence Identity But Different Folds.
Proc. Natl. Acad. Sci. Usa V. 105 2343 2008
PubMed-ID: 18227506  |  Reference-DOI: 10.1073/PNAS.0711589105

(-) Compounds

Molecule 1 - PROPHAGE PFL 6 CRO
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PROPHAGE PFL 6 CRO
    Organism Scientific: PSEUDOMONAS FLUORESCENS
    Organism Taxid: 220664
    Strain: PF-5

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1BCT1Ligand/IonBICARBONATE ION
2DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3MSE4Mod. Amino AcidSELENOMETHIONINE
4SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:35 , TYR B:45 , GLU B:46 , HOH B:717BINDING SITE FOR RESIDUE SO4 B 501
2AC2SOFTWARELYS A:3 , LYS B:3 , SER B:31 , ARG B:35BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWARELYS B:3 , GLN B:32 , ARG B:35 , HOH B:711BINDING SITE FOR RESIDUE SO4 B 503
4AC4SOFTWAREARG A:56 , ILE A:58 , LYS B:8 , ARG B:38 , HOH B:722BINDING SITE FOR RESIDUE SO4 B 504
5AC5SOFTWAREASN A:26 , GLN A:27 , SER A:28 , HOH A:627BINDING SITE FOR RESIDUE BCT A 601
6AC6SOFTWARESER B:7 , GLY B:24 , ASN B:26 , HOH B:726 , HOH B:727BINDING SITE FOR RESIDUE DTT B 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:58 -Pro A:59
2Ile B:58 -Pro B:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PIJ)

(-) 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:59
 aligned with J3IU59_9PSED | J3IU59 from UniProtKB/TrEMBL  Length:67

    Alignment length:59
                                    10        20        30        40        50         
          J3IU59_9PSED    1 MKKIPLSKYLEEHGTQAALAAALGVNQSAISQMVRAGRSIEITLHNDGRIEANEIRPIP 59
               SCOP domains d2pija_ A: automated matches                                SCOP domains
               CATH domains -2pijA00 A:2-59 lambda repressor-like DNA-binding domains   CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhh.hhhhhhhhhh.hhhhhhhhhhh...eeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                  2pij A  1 mKKIPLSKYLEEHGTQSALAAALGVNQSAISQmVRAGRSIEITLYEDGRVEANEIRPIP 59
                            |       10        20        30  |     40        50         
                            |                              33-MSE                      
                            1-MSE                                                      


Chain B from PDB  Type:PROTEIN  Length:60
 aligned with J3IU59_9PSED | J3IU59 from UniProtKB/TrEMBL  Length:67

    Alignment length:60
                                    10        20        30        40        50        60
          J3IU59_9PSED    1 MKKIPLSKYLEEHGTQAALAAALGVNQSAISQMVRAGRSIEITLHNDGRIEANEIRPIPA 60
               SCOP domains d2pijb_ B: automated matches                                 SCOP domains
               CATH domains -2pijB00 B:2-60 lambda repressor-like DNA-binding domains    CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeehhhhhhhh.hhhhhhhhhh.hhhhhhhhhhh...eeeee.....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  2pij B  1 mKKIPLSKYLEEHGTQSALAAALGVNQSAISQmVRAGRSIEITLYEDGRVEANEIRPIPA 60
                            |       10        20        30  |     40        50        60
                            1-MSE                          33-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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (J3IU59_9PSED | J3IU59)
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.

 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
    BCT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DTT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ile A:58 - Pro A:59   [ RasMol ]  
    Ile B:58 - Pro B:59   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  2pij
    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
  J3IU59_9PSED | J3IU59
    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
  J3IU59_9PSED | J3IU59
    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 2PIJ)

(-) Related Entries Specified in the PDB File

3bd1 STRUCTURE OF A HOMOLOGOUS PROTEIN WITH A DIFFERENT FOLD