2NYG

Crystal structure of YokD protein from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of YokD protein from Bacillus subtilis

Madegowda, M.Eswaramoorthy, S.Burley, S.K.Swaminathan, S.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YokD protein
A, B, C, D, E, F
273Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: yokD
EC: 2.3.1.-
Find proteins for O32003 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O32003
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download SDF File 
Download CCD File 
A, B, C, D, E
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.257 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.020α = 90.00
b = 132.390β = 90.00
c = 185.800γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
SOLVEphasing
CNSrefinement
SHARPphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-09-13
    Type: Refinement description