4BJO | pdb_00004bjo

Nitrate in the active site of PTP1b is a putative mimetic of the transition state

• PDB DOI: https://doi.org/10.2210/pdb4BJO/pdb

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


• Deposited: 2013-04-19 Released: 2014-02-12 
• Deposition Author(s): Kenny, P.W., Newman, J., Peat, T.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.239 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.215 (Depositor) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Nitrate in the Active Site of Protein Tyrosine Phosphatase 1B is a Putative Mimetic of the Transition State.

Kenny, P.W., Newman, J., Peat, T.S.

(2014) Acta Crystallogr D Biol Crystallogr 70: 565

• PubMed: 24531490 
• DOI: https://doi.org/10.1107/S1399004713031052
• Primary Citation Related Structures: 
  4BJO


• PubMed Abstract: 
  

  The X-ray crystal structure of the complex of protein tyrosine phosphatase 1B with nitrate anion has been determined and modelled quantum-mechanically. Two protomers were present in the structure, one with the mechanistically important WPD loop closed and the other with this loop open. Nitrate was observed bound to each protomer, making close contacts with the S atom of the catalytic cysteine and a tyrosine residue from a crystallographically related protomer.

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Organizational Affiliation: 
• CSIRO Materials, Science and Engineering, 343 Royal Parade, Parkville, VIC 3052, Australia.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 79.07 kDa 
• Atom Count: 4,862 
• Modeled Residue Count: 571 
• Deposited Residue Count: 676 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1	A, B	338	Homo sapiens	Mutation(s): 0  EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens) Explore P18031  Go to UniProtKB:  P18031
PHAROS:  P18031 GTEx:  ENSG00000196396

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	F [auth A], K [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL	C [auth A], D [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.239 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.215 (Depositor) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.62	α = 90
b = 66.765	β = 95.01
c = 68.771	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): Kenny, P.W., Newman, J., Peat, T.S.

Revision History  

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 1.1: 2014-02-26
  Changes: Database references
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description