Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE CRO PROTEIN FROM PUTATIVE PROPHAGE ELEMENT XFASO 1 IN XYLELLA FASTIDIOSA STRAIN ANN-1
 
Authors :  B. M. Hall, S. A. Roberts, W. R. Montfort, M. H. Cordes
Date :  13 Nov 07  (Deposition) - 25 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Biol. Unit 2:  A,B,C  (1x)
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 - CRO PROTEIN
    Chains: A, B, C
    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
    Organism Scientific: XYLELLA FASTIDIOSA
    Organism Taxid: 155920
    Strain: ANN-1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
3SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO C:38 , ALA C:39 , ARG C:59 , HOH C:201 , HOH C:220BINDING SITE FOR RESIDUE SO4 C 160
2AC2SOFTWAREPRO C:38 , ALA C:39 , ARG C:59 , HOH C:201BINDING SITE FOR RESIDUE SO4 C 161
3AC3SOFTWAREGLY A:12 , LYS C:10 , SER C:29 , ARG C:32 , ASN C:50BINDING SITE FOR RESIDUE CL C 162
4AC4SOFTWAREPRO A:38 , ALA A:39 , GLU A:40 , ARG A:59 , ALA B:39 , ARG B:59BINDING SITE FOR RESIDUE GOL A 156
5AC5SOFTWARESER A:15 , GLN A:25 , HOH A:180 , HOH A:203 , ARG B:24 , GLN B:25 , SER B:26BINDING SITE FOR RESIDUE GOL A 157
6AC6SOFTWAREASP A:5 , ILE A:6 , ASN A:9 , ASN C:2 , ASN C:9BINDING SITE FOR RESIDUE GOL C 158
7AC7SOFTWAREARG B:34 , ARG B:36 , PRO B:38BINDING SITE FOR RESIDUE GOL B 159

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BD1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BD1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BD1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BD1)

(-) Exons   (0, 0)

(no "Exon" information available for 3BD1)

(-) 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:65
                                                                                                
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains 3bd1A00 A:1-65 lambda repressor-like DNA-binding domains          CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  3bd1 A  1 MNAIDIAINKLGSVSALAASLGVRQSAISNWRARGRVPAERCIDIERVTNGAVICRELRPDVFGA 65
                                    10        20        30        40        50        60     


Chain B from PDB  Type:PROTEIN  Length:63
                                                                                              
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains 3bd1B00 B:1-63 lambda repressor-like DNA-binding domains        CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  3bd1 B  1 MNAIDIAINKLGSVSALAASLGVRQSAISNWRARGRVPAERCIDIERVTNGAVICRELRPDVF 63
                                    10        20        30        40        50        60   


Chain C from PDB  Type:PROTEIN  Length:64
                                                                                               
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains 3bd1C00 C:1-64 lambda repressor-like DNA-binding domains         CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  3bd1 C  1 MNAIDIAINKLGSVSALAASLGVRQSAISNWRARGRVPAERCIDIERVTNGAVICRELRPDVFG 64
                                    10        20        30        40        50        60
   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 3BD1)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BD1)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3BD1)

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3bd1)
 
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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  3bd1
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3BD1)

(-) Related Entries Specified in the PDB File

2pij STRUCTURE OF THE CRO PROTEIN FROM PROPHAGE PFL 6 IN PSEUDOMONAS FLUORESCENS PF-5