8YHI | pdb_00008yhi

The Crystal Structure of SHP1 from Biortus.

• PDB DOI: https://doi.org/10.2210/pdb8YHI/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-28 Released: 2024-03-13 
• Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Qi, J., Shen, Z.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.200 (DCC) 

Starting Model: experimental

Literature

The Crystal Structure of SHP1 from Biortus.

Wang, F., Cheng, W., Yuan, Z., Qi, J., Shen, Z.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.23 kDa 
• Atom Count: 2,470 
• Modeled Residue Count: 280 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 6	A	288	Homo sapiens	Mutation(s): 0  Gene Names: PTPN6, HCP, PTP1C EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P29350 (Homo sapiens) Explore P29350  Go to UniProtKB:  P29350
PHAROS:  P29350 GTEx:  ENSG00000111679

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.200 (DCC) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.302	α = 90
b = 56.498	β = 90
c = 110.258	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-13 
Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Qi, J., Shen, Z.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-03-13
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary