5N0L

The structure of the cofactor binding GAF domain of the nutrient sensor CodY from Clostridium difficile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Impact of CodY protein on metabolism, sporulation and virulence in Clostridioides difficile ribotype 027

Levdikov, V.M.Blagova, E.V.Wilkinson, A.J.Sonenshein, A.L.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTP-sensing transcriptional pleiotropic repressor CodY
A, B, C, D, E, F
159Peptoclostridium difficile (strain 630)Mutation(s): 0 
Gene Names: codY
Find proteins for Q18BE1 (Peptoclostridium difficile (strain 630))
Go to UniProtKB:  Q18BE1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ILE
Query on ILE

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ISOLEUCINE
C6 H13 N O2
AGPKZVBTJJNPAG-WHFBIAKZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.154 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 120.890α = 90.00
b = 190.390β = 90.00
c = 43.510γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesGM042219

Revision History 

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 2.0: 2018-11-21
    Type: Atomic model, Data collection, Derived calculations