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(-) Description

Title :  RADIATION DAMAGE TO THE NUCLEOPROTEIN COMPLEX C.ESP1396I: DOSE (DWD) 6.2 MGY
 
Authors :  C. S. Bury, J. E. Mcgeehan, E. F. Garman
Date :  02 Dec 14  (Deposition) - 11 Mar 15  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Protein-Dna Complex, Radiation Damage, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Bury, E. F. Garman, H. M. Ginn, R. B. Ravelli, I. Carmichael, G. Kneale, J. E. Mcgeehan
Radiation Damage To Nucleoprotein Complexes In Macromolecular Crystallography.
J. Synchrotron Radiat. V. 22 213 2015
PubMed-ID: 25723923  |  Reference-DOI: 10.1107/S1600577514026289
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATORY PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET23
    Expression System Taxid: 469008
    Expression System Variant: GOLD
    Expression System Vector Type: PLASMID
    Gene: ESP1396IC
    Organism Scientific: ENTEROBACTER SP. RFL1396
    Organism Taxid: 211595
    Synonym: CONTROLLER PROTEIN
 
Molecule 2 - 35-MER DNA
    Chains: E
    Engineered: YES
    Fragment: OPERATOR DNA
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: CHEMICALLY SYNTHESISED DNA
    Synthetic: YES
 
Molecule 3 - 35-MER DNA
    Chains: F
    Engineered: YES
    Fragment: OPERATOR DNA
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: CHEMICALLY SYNTHESISED DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4X4C)

(-) Sites  (0, 0)

(no "Site" information available for 4X4C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X4C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4X4C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X4C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X4C)

(-) Exons   (0, 0)

(no "Exon" information available for 4X4C)

(-) 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:76
                                                                                                           
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  4x4c A  2 ESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILK 77
                                    11        21        31        41        51        61        71      


Chain B from PDB  Type:PROTEIN  Length:77
                                                                                                            
               SCOP domains ----------------------------------------------------------------------------- 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
                  4x4c B  2 ESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILKH 78
                                    11        21        31        41        51        61        71       


Chain C from PDB  Type:PROTEIN  Length:77
                                                                                                            
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                  4x4c C  2 ESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILKH 78
                                    11        21        31        41        51        61        71       


Chain D from PDB  Type:PROTEIN  Length:76
                                                                                                           
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  4x4c D  2 ESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILK 77
                                    11        21        31        41        51        61        71      


Chain E from PDB  Type:DNA  Length:35
                                                                  
                  4x4c E  1 ATGTGACTTATAGTCCGTGTGATTATAGTCAACAT 35
                                    10        20        30     


Chain F from PDB  Type:DNA  Length:35
                                                                  
                  4x4c F  1 ATGTTGACTATAATCACACGGACTATAAGTCACAT 35
                                    10        20        30
   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 4X4C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X4C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X4C)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4x4c)
 

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 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 4ivz 4iwr 4x4b 4x4d 4x4e 4x4f 4x4g 4x4h 4x4i

(-) Related Entries Specified in the PDB File

3clc THE NEW STRUCTURE IS PART OF A RADIATION DAMAGE STUDY ON THE PROTEIN-DNA COMPLEX WITH PDB CODE 3CLC
4x4b IN THIS RADIATION DAMAGE STUDY, 4X4B IS THE SAME PROTEIN-DNA COMPLEX AT A DOSE (DWD) OF 2.1MGY