3PXH | pdb_00003pxh

Tandem Ig domains of tyrosine phosphatase LAR

• PDB DOI: https://doi.org/10.2210/pdb3PXH/pdb

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


• Deposited: 2010-12-09 Released: 2011-03-23 
• Deposition Author(s): Biersmith, B.H., Bouyain, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.240 (Depositor) 
• R-Value Work: 
  0.220 (Depositor) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

The Immunoglobulin-like Domains 1 and 2 of the Protein Tyrosine Phosphatase LAR Adopt an Unusual Horseshoe-like Conformation.

Biersmith, B.H., Hammel, M., Geisbrecht, E.R., Bouyain, S.

(2011) J Mol Biology 408: 616-627

• PubMed: 21402080 
• DOI: https://doi.org/10.1016/j.jmb.2011.03.013
• Primary Citation Related Structures: 
  3PXH, 3PXJ


• PubMed Abstract: 
  

  Neurogenesis depends on exquisitely regulated interactions between macromolecules on the cell surface and in the extracellular matrix. In particular, interactions between proteoglycans and members of the type IIa subgroup of receptor protein tyrosine phosphatases underlie crucial developmental processes such as the formation of synapses at the neuromuscular junction and the migration of axons to their appropriate targets. We report the crystal structures of the first and second immunoglobulin-like domains of the Drosophila type IIa receptor Dlar and its mouse homolog LAR. These two domains adopt an unusual antiparallel arrangement that has not been reported in tandem repeats of immunoglobulin-like domains and that is presumably conserved in all type IIa receptor protein tyrosine phosphatases.

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Organizational Affiliation: 
• Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, 5100 Rockhill Road, Kansas City, MO 64110, USA.

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: 21.82 kDa 
• Atom Count: 1,589 
• Modeled Residue Count: 197 
• Deposited Residue Count: 201 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-type tyrosine-protein phosphatase F	A	201	Mus musculus	Mutation(s): 0  Gene Names: Ptprf, Lar EC: 3.1.3.48
UniProt
Find proteins for A2A8L5 (Mus musculus) Explore A2A8L5  Go to UniProtKB:  A2A8L5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.240 (Depositor) 
• R-Value Work:  0.220 (Depositor) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.45	α = 90
b = 77.45	β = 90
c = 68.499	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-23 
Deposition Author(s): Biersmith, B.H., Bouyain, S.

Revision History  

• Version 1.0: 2011-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary