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 :  A Y37F MUTANT OF C.ESP1396I BOUND TO ITS HIGHEST AFFINITY OPERATOR SITE OM
 
Authors :  R. N. A. Martin, J. E. Mcgeehan, G. G. Kneale
Date :  23 Jan 13  (Deposition) - 29 Jan 14  (Release) - 18 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Restriction-Modification, Helix-Turn-Helix, Transcriptional Regulator, Dna, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. N. Martin, J. E. Mcgeehan, G. Kneale
Structural And Mutagenic Analysis Of The Rm Controller Protein C. Esp1396I.
Plos One V. 9 98365 2014
PubMed-ID: 24887147  |  Reference-DOI: 10.1371/JOURNAL.PONE.0098365
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATORY PROTEIN
    Chains: A, B, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ESP1396IC
    Mutation: YES
    Organism Scientific: ENTEROBACTER SP.
    Organism Taxid: 211595
    Strain: RFL1396
 
Molecule 2 - DNA (5'- D(*AP*TP*GP*TP*AP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*GP*AP*CP*A)-3')
    Chains: C, G
    Engineered: YES
    Other Details: 19 BASE OM OPERATOR
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*TP*TP*GP*TP*CP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*TP*AP*CP*A)-3')
    Chains: D, H
    Engineered: YES
    Other Details: 19 BASE OM OPERATOR COMPLEMENT
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4IVZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu F:19 -Lys F:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IVZ)

(-) 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:76
                                                                                                           
               SCOP domains d4ivza_ A: automated matches                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  4ivz A  2 ESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTFISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILK 77
                                    11        21        31        41        51        61        71      


Chain B from PDB  Type:PROTEIN  Length:76
                                                                                                           
               SCOP domains d4ivzb_ B: automated matches                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  4ivz B  2 ESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTFISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILK 77
                                    11        21        31        41        51        61        71      


Chain C from PDB  Type:DNA  Length:19
                                                  
                  4ivz C  1 ATGTAGACTATAGTCGACA 19
                                    10         


Chain D from PDB  Type:DNA  Length:19
                                                  
                  4ivz D  1 TTGTCGACTATAGTCTACA 19
                                    10         


Chain E from PDB  Type:PROTEIN  Length:77
                                                                                                            
               SCOP domains d4ivze_ E: automated matches                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                  4ivz E  2 ESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTFISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILKH 78
                                    11        21        31        41        51        61        71       


Chain F from PDB  Type:PROTEIN  Length:76
                                                                                                           
               SCOP domains d4ivzf_ F: automated matches                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  4ivz F  2 ESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTFISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILK 77
                                    11        21        31        41        51        61        71      


Chain G from PDB  Type:DNA  Length:19
                                                  
                  4ivz G  1 ATGTAGACTATAGTCGACA 19
                                    10         


Chain H from PDB  Type:DNA  Length:19
                                                  
                  4ivz H  1 TTGTCGACTATAGTCTACA 19
                                    10
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4ivz)
 
  Sites
(no "Sites" information available for 4ivz)
 
  Cis Peptide Bonds
    Glu F:19 - Lys F:20   [ RasMol ]  
 
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
  4ivz
    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
  Q8GGH0_9ENTR | Q8GGH0
    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
  Q8GGH0_9ENTR | Q8GGH0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8GGH0_9ENTR | Q8GGH0: 3clc 3fya 3g5g 3s8q 3ufd 4f8d 4fbi 4fn3 4i6r 4i6t 4i6u 4i8t 4ia8 4iwr 4x4b 4x4c 4x4d 4x4e 4x4f 4x4g 4x4h 4x4i

(-) Related Entries Specified in the PDB File

3clc NATIVE DNA BOUND TETRAMER
3fya R35A MUTANT FREE PROTEIN
3g5g NATIVE FREE PROTEIN
3s8q NATIVE DNA BOUND DIMER (OL)
3ufd NATIVE DNA BOUND DIMER (OM)
4f8d R46A MUTANT FREE PROTEIN
4fbi R46A MUTANT FREE PROTEIN
4fn3 S52A MUTANT FREE PROTEIN
4i6r NATIVE FREE PROTEIN (HIGH RESOLUTION)
4i6t T36A MUTANT FREE PROTEIN
4i6u Y37F MUTANT FREE PROTEIN
4i8t NATIVE DNA BOUND DIMER (OR)
4ia8 Y37A MUTANT FREE PROTEIN