4H34 | pdb_00004h34

Crystal structure of the tyrosine phosphatase SHP-2 with Q506P mutation

• PDB DOI: https://doi.org/10.2210/pdb4H34/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-09-13 Released: 2013-10-02 
• Deposition Author(s): Qiu, W., Lin, A., Hutchinson, A., Romanov, V., Ruzanov, M., Thompson, C., Lam, K., Kisselman, G., Battaile, K., Chirgadze, N.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.242 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the tyrosine phosphatase SHP-2 with Q506P mutation

Qiu, W., Lin, A., Hutchinson, A., Romanov, V., Ruzanov, M., Thompson, C., Lam, K., Kisselman, G., Battaile, K., Chirgadze, N.Y.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 64.97 kDa 
• Atom Count: 4,041 
• Modeled Residue Count: 486 
• Deposited Residue Count: 560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 11	A	560	Homo sapiens	Mutation(s): 1  Gene Names: PTPN11, PTP2C, SHPTP2 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q06124 (Homo sapiens) Explore Q06124  Go to UniProtKB:  Q06124
PHAROS:  Q06124 GTEx:  ENSG00000179295

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.242 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.79	α = 90
b = 202.35	β = 90
c = 44.46	γ = 90

Software Package:

Software Name	Purpose
JBluIce-EPICS	data collection
PHASER	phasing
BUSTER	refinement
XDS	data reduction
XSCALL	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): Qiu, W., Lin, A., Hutchinson, A., Romanov, V., Ruzanov, M., Thompson, C., Lam, K., Kisselman, G., Battaile, K., Chirgadze, N.Y.

Revision History  

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description