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 RESTRICTION-MODIFICATION CONTROLLER PROTEIN C.CSP231I OL OPERATOR COMPLEX
 
Authors :  M. B. Shevtsov, S. D. Streeter, S. J. Thresh, J. E. Mcgeehan, G. G. Kneale
Date :  20 Mar 13  (Deposition) - 02 Apr 14  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,G,H  (1x)
Biol. Unit 2:  C,D,E,F  (1x)
Keywords :  Helix-Turn-Helix, C Controller Protein, Restriction-Modification Systems, Transcriptional Regulation, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. B. Shevtsov, S. D. Streeter, S. J. Thresh, A. Swiderska, J. E. Mcgeehan, G. G. Kneale
Structural Analysis Of Dna Binding By C. Csp231I, A Member O A Novel Class Of R-M Controller Proteins Regulating Gene Expression.
Acta Crystallogr. , Sect. D V. 71 398 2015
PubMed-ID: 25664751  |  Reference-DOI: 10.1107/S139900471402690X

(-) Compounds

Molecule 1 - CSP231I C PROTEIN
    Chains: A, B, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21(DE3) GOLD
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: CITROBACTER SP. RFL231
    Organism Taxid: 315237
 
Molecule 2 - DNA (5'- D(*AP*CP*AP*CP*TP*AP*AP*GP*GP*AP*AP*AP*AP*CP*TP*TP*AP*GP*TP*AP*A)- 3')
    Chains: C, G
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*TP*TP*AP*CP*TP*AP*AP*GP*TP*TP*TP*TP*CP*CP*TP*TP*AP*GP*TP*GP*T)- 3')
    Chains: D, H
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB    GH
Biological Unit 2 (1x):   CDEF  

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4JQD)

(-) Sites  (0, 0)

(no "Site" information available for 4JQD)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JQD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JQD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JQD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JQD)

(-) Exons   (0, 0)

(no "Exon" information available for 4JQD)

(-) 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:94
                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  4jqd A  1 MLIRRLKDARLRAGISQEKLGVLAGIDEASASARMNQYEKGKHAPDFEMANRLAKVLKIPVSYLYTPEDDLAQIILTWNELNEQERKRINFYIR 94
                                    10        20        30        40        50        60        70        80        90    


Chain B from PDB  Type:PROTEIN  Length:94
                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  4jqd B  1 MLIRRLKDARLRAGISQEKLGVLAGIDEASASARMNQYEKGKHAPDFEMANRLAKVLKIPVSYLYTPEDDLAQIILTWNELNEQERKRINFYIR 94
                                    10        20        30        40        50        60        70        80        90    


Chain C from PDB  Type:DNA  Length:21
                                                    
                  4jqd C  1 ACACTAAGGAAAACTTAGTAA 21
                                    10        20 


Chain D from PDB  Type:DNA  Length:21
                                                    
                  4jqd D  1 TTACTAAGTTTTCCTTAGTGT 21
                                    10        20 


Chain E from PDB  Type:PROTEIN  Length:97
                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                  4jqd E  1 MLIRRLKDARLRAGISQEKLGVLAGIDEASASARMNQYEKGKHAPDFEMANRLAKVLKIPVSYLYTPEDDLAQIILTWNELNEQERKRINFYIRKKA 97
                                    10        20        30        40        50        60        70        80        90       


Chain F from PDB  Type:PROTEIN  Length:93
                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  4jqd F  1 MLIRRLKDARLRAGISQEKLGVLAGIDEASASARMNQYEKGKHAPDFEMANRLAKVLKIPVSYLYTPEDDLAQIILTWNELNEQERKRINFYI 93
                                    10        20        30        40        50        60        70        80        90   


Chain G from PDB  Type:DNA  Length:21
                                                    
                  4jqd G  1 ACACTAAGGAAAACTTAGTAA 21
                                    10        20 


Chain H from PDB  Type:DNA  Length:21
                                                    
                  4jqd H  1 TTACTAAGTTTTCCTTAGTGT 21
                                    10        20
   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 4JQD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JQD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JQD)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

 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 4jqd)
 
  Sites
(no "Sites" information available for 4jqd)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4jqd)
 
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
  4jqd
    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
  Q32WH4_9ENTR | Q32WH4
    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
  Q32WH4_9ENTR | Q32WH4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q32WH4_9ENTR | Q32WH4: 3lfp 3lis 4jcx 4jcy

(-) Related Entries Specified in the PDB File

3lfp FREE NON-COMPLEXED C.CSP231I PROTEIN DIMER
3lis FREE NON-COMPLEXED C.CSP231I PROTEIN DIMER (MONOCLINIC FORM)
4jcx C.CSP231I OL OPERATOR COMPLEX
4jcy C.CSP231I OR OPERATOR COMPLEX