2B0C | pdb_00002b0c

The crystal structure of the putative phosphatase from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb2B0C/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-09-13 Released: 2005-11-22 
• Deposition Author(s): Zhang, R., Skarina, T., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.259 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

The 2.0A crystal structure of the putative phosphatase from Escherichia coli

Zhang, R., Skarina, T., Savchenko, A., Edwards, A., Joachimiak, A.

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: 23.86 kDa 
• Atom Count: 1,782 
• Modeled Residue Count: 199 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative phosphatase	A	206	Escherichia coli K-12	Mutation(s): 0  Gene Names: yihX EC: 3.1.3.10
UniProt
Find proteins for P0A8Y3 (Escherichia coli (strain K12)) Explore P0A8Y3  Go to UniProtKB:  P0A8Y3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G1P	B [auth A]	1-O-phosphono-alpha-D-glucopyranose C6 H13 O9 P HXXFSFRBOHSIMQ-VFUOTHLCSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.259 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.256	α = 90
b = 62.256	β = 90
c = 127.038	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-22 
Deposition Author(s): Zhang, R., Skarina, T., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2005-11-22
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-12-25
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary