3E5U | pdb_00003e5u

OCPA complexed CprK (C200S)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 
    0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3C4Click on this verticalbar to view details

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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic nucleotide-binding proteinA [auth C],
B [auth A],
C [auth D],
D [auth B]
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3C4
Query on 3C4

Download Ideal Coordinates CCD File 
E [auth C],
G [auth A],
H [auth A],
J [auth D],
L [auth B]
(3-CHLORO-4-HYDROXYPHENYL)ACETIC ACID
C8 H7 Cl O3
IYTUKSIOQKTZEG-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth C],
K [auth D],
M [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.141α = 90
b = 117.17β = 94.65
c = 84.876γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3C4Click on this verticalbar to view details

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