2I42 | pdb_00002i42

Crystal structure of Yersinia protein tyrosine phosphatase complexed with vanadate, a transition state analogue

• PDB DOI: https://doi.org/10.2210/pdb2I42/pdb

• Classification: HYDROLASE
• Organism(s): Yersinia enterocolitica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-08-21 Released: 2006-09-19 
• Deposition Author(s): Vijayalakshmi, J., Saper, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 
  0.170 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of Yersinia protein tyrosine phosphatase complexed with vanadate, a transition state analogue

Vijayalakshmi, J., Saper, M.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.67 kDa 
• Atom Count: 2,355 
• Modeled Residue Count: 282 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase	A	306	Yersinia enterocolitica	Mutation(s): 0  Gene Names: yopH, yop51 EC: 3.1.3.48
UniProt
Find proteins for P15273 (Yersinia enterocolitica) Explore P15273  Go to UniProtKB:  P15273

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VO4	B [auth A]	VANADATE ION O4 V LSGOVYNHVSXFFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work:  0.170 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.39	α = 90
b = 49.66	β = 90
c = 100.39	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
MADNESS	data collection
XSCALE	data scaling
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-19 
Deposition Author(s): Vijayalakshmi, J., Saper, M.A.

Revision History  

• Version 1.0: 2006-09-19
  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: 2013-05-29
  Changes: Non-polymer description
• Version 1.4: 2017-10-18
  Changes: Advisory, Refinement description
• Version 1.5: 2023-08-30
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description