5GYN

Crystal structure of human pyridoxal 5'-phosphate phosphatase (Chronophin) mutant - C221S

• PDB DOI: https://doi.org/10.2210/pdb5GYN/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-09-23 Released: 2017-09-27 
• Deposition Author(s): Lee, H.J., Cho, H.J., Kang, B.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.234 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 

Literature

Crystal structure of human pyridoxal 5'-phosphate phosphatase (Chronophin) mutant - C221S

Lee, H.J., Cho, H.J., Kang, B.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.22 kDa 
• Atom Count: 2,403 
• Modelled Residue Count: 295 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal phosphate phosphatase	A	301	Homo sapiens	Mutation(s): 1  Gene Names: PDXP, CIN, PLP, PLPP EC: 3.1.3.3 (PDB Primary Data), 3.1.3.74 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96GD0 (Homo sapiens) Explore Q96GD0  Go to UniProtKB:  Q96GD0
PHAROS:  Q96GD0 GTEx:  ENSG00000241360

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.234 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.578	α = 90
b = 54.578	β = 90
c = 214.697	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-27 
Deposition Author(s): Lee, H.J., Cho, H.J., Kang, B.S.

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description