2NYG | pdb_00002nyg

Crystal structure of YokD protein from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb2NYG/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-11-20 Released: 2006-12-12 
• Deposition Author(s): Madegowda, M., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.296 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Literature

Crystal structure of YokD protein from Bacillus subtilis

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 189.97 kDa 
• Atom Count: 12,534 
• Modeled Residue Count: 1,567 
• Deposited Residue Count: 1,638 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YokD protein	A, B, C, D, E, F	273	Bacillus subtilis	Mutation(s): 0  Gene Names: yokD EC: 2.3.1
UniProt
Find proteins for O32003 (Bacillus subtilis (strain 168)) Explore O32003  Go to UniProtKB:  O32003

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.296 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.02	α = 90
b = 132.39	β = 90
c = 185.8	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-12 
Deposition Author(s): Madegowda, M., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-12-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-09-13
  Changes: Refinement description
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references