4N5U | pdb_00004n5u

Crystal structure of the 4th FN3 domain of human Protein Tyrosine phosphatase, receptor type F [PSI-NYSGRC-006240]

• PDB DOI: https://doi.org/10.2210/pdb4N5U/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2013-10-10 Released: 2013-10-30 
• Deposition Author(s): Kumar, P.R., Banu, R., Bhosle, R., Calarese, D.A., Celikgil, A., Chamala, S., Chan, M.K., Chowdhury, S., Fiser, A., Garforth, S.J., Glenn, A.S., Hillerich, B., Khafizov, K., Attonito, J., Love, J.D., Patel, H., Patel, R., Seidel, R.D., Smith, B., Stead, M., Toro, R., Casadevall, A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the 4th FN3 domain of human PTP, receptor F [PSI-NYSGRC-006240]

Kumar, P.R., Casadevall, A., Almo, S.C.

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: 13.1 kDa 
• Atom Count: 1,015 
• Modeled Residue Count: 108 
• Deposited Residue Count: 117 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-type tyrosine-protein phosphatase F	A	117	Homo sapiens	Mutation(s): 0  Gene Names: LAR, PTPRF EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P10586 (Homo sapiens) Explore P10586  Go to UniProtKB:  P10586
PHAROS:  P10586 GTEx:  ENSG00000142949

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: 1.46 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.011	α = 90
b = 39.677	β = 90
c = 68.525	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-30 
Deposition Author(s): Kumar, P.R., Banu, R., Bhosle, R., Calarese, D.A., Celikgil, A., Chamala, S., Chan, M.K., Chowdhury, S., Fiser, A., Garforth, S.J., Glenn, A.S., Hillerich, B., Khafizov, K., Attonito, J., Love, J.D., Patel, H., Patel, R., Seidel, R.D., Smith, B., Stead, M., Toro, R., Casadevall, A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

Revision History  

• Version 1.0: 2013-10-30
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description