3NP5 | pdb_00003np5

Crystal structure of an abridged form of the mature ectodomain of the human receptor-type protein tyrosine phosphatase ICA512/IA-2 AT pH 4.5

• PDB DOI: https://doi.org/10.2210/pdb3NP5/pdb

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


• Deposited: 2010-06-27 Released: 2010-12-29 
• Deposition Author(s): Primo, M.E., Jakoncic, J., Poskus, E., Ermacora, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.239 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

Receptor-Type Protein-Tyrosine Phosphatase Ia-2-Ica512

Primo, M.E., Jakoncic, J., Poskus, E., Ermacora, M.R.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.63 kDa 
• Atom Count: 2,874 
• Modeled Residue Count: 353 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-type tyrosine-protein phosphatase-like N	A, B, C, D	89	Homo sapiens	Mutation(s): 0  Gene Names: ICA3, ICA512, PTPRN
UniProt & NIH Common Fund Data Resources
Find proteins for Q16849 (Homo sapiens) Explore Q16849  Go to UniProtKB:  Q16849
PHAROS:  Q16849 GTEx:  ENSG00000054356

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.239 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.180 (DCC) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.662	α = 90
b = 44.662	β = 90
c = 168.665	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-29 
Deposition Author(s): Primo, M.E., Jakoncic, J., Poskus, E., Ermacora, M.R.

Revision History  

• Version 1.0: 2010-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-04-18
  Changes: Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description