3E6C | pdb_00003e6c

CprK OCPA DNA Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.250 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Molecular basis of halorespiration control by CprK, a CRP-FNR type transcriptional regulator

Levy, C.Pike, K.Heyes, D.J.Joyce, M.G.Gabor, K.Smidt, H.van der Oost, J.Leys, D.

(2008) Mol Microbiol 70: 151-167

  • DOI: https://doi.org/10.1111/j.1365-2958.2008.06399.x
  • Primary Citation Related Structures: 
    3E5Q, 3E5U, 3E5X, 3E6B, 3E6C, 3E6D

  • PubMed Abstract: 

    Certain bacteria are able to conserve energy via the reductive dehalogenation of halo-organic compounds in a respiration-type metabolism. The transcriptional regulator CprK from Desulfitobacterium spp. induces expression of halorespiratory genes upon binding of o-chlorophenol ligands and is reversibly inactivated by oxygen through disulphide bond formation. We report crystal structures of D. hafniense CprK in the ligand-free (both oxidation states), ligand-bound (reduced) and DNA-bound states, making it the first member of the widespread CRP-FNR superfamily for which a complete structural description of both redox-dependent and allosteric molecular rearrangements is available. In conjunction with kinetic and thermodynamic ligand binding studies, we provide a model for the allosteric mechanisms underpinning transcriptional control. Amino acids that play a key role in this mechanism are not conserved in functionally distinct CRP-FNR members. This suggests that, despite significant structural homology, distinct allosteric mechanisms are used, enabling this protein family to control a very wide range of processes.


  • Organizational Affiliation
    • Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, UK.

Macromolecule Content 

  • Total Structure Weight: 36.51 kDa 
  • Atom Count: 2,506 
  • Modeled Residue Count: 251 
  • Deposited Residue Count: 276 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyclic nucleotide-binding proteinA [auth C]250Desulfitobacterium hafniense DCB-2Mutation(s): 1 
Gene Names: Dhaf_0678
UniProt
Find proteins for B8FW11 (Desulfitobacterium hafniense (strain DSM 10664 / DCB-2))
Explore B8FW11 
Go to UniProtKB:  B8FW11
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8FW11
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*DGP*DCP*DAP*DTP*DTP*DAP*DAP*DCP*DAP*DTP*DGP*DCP*DC)-3')13N/A
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*DGP*DGP*DCP*DAP*DTP*DGP*DTP*DTP*DAP*DAP*DTP*DGP*DC)-3')C [auth A]13N/A
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3C4

Query on 3C4



Download:Ideal Coordinates CCD File
D [auth C](3-CHLORO-4-HYDROXYPHENYL)ACETIC ACID
C8 H7 Cl O3
IYTUKSIOQKTZEG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.250 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.6α = 90
b = 100.6β = 90
c = 149.66γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2008-09-30 
  • Deposition Author(s): Levy, C.

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-02-21
    Changes: Data collection