4ETM | pdb_00004etm

Crystal structure of YfkJ from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb4ETM/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-24 Released: 2012-10-24 
• Deposition Author(s): Cao, X.F., Su, X.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.248 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of YfkJ from Bacillus subtilis

Cao, X.F., Su, X.D.

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.

Macromolecule Content 

• Total Structure Weight: 38.22 kDa 
• Atom Count: 2,906 
• Modeled Residue Count: 321 
• Deposited Residue Count: 346 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low molecular weight protein-tyrosine-phosphatase yfkJ	A, B	173	Bacillus subtilis	Mutation(s): 0  Gene Names: yfkJ, BSU07880 EC: 3.1.3.48
UniProt
Find proteins for O35016 (Bacillus subtilis (strain 168)) Explore O35016  Go to UniProtKB:  O35016

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	E [auth A], H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA	D [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.248 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.152	α = 90
b = 52.922	β = 102.84
c = 86.609	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-24 
Deposition Author(s): Cao, X.F., Su, X.D.

Revision History  

• Version 1.0: 2012-10-24
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description