4JQP | pdb_00004jqp

X-ray crystal structure of a 4-hydroxythreonine-4-phosphate dehydrogenase from Burkholderia phymatum

• PDB DOI: https://doi.org/10.2210/pdb4JQP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Paraburkholderia phymatum STM815
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-03-20 Released: 2013-04-17 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.174 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of a 4-hydroxythreonine-4-phosphate dehydrogenase from Burkholderia phymatum

Fairman, J.W., Clifton, M.C., Edwards, T.E., Lorimer, D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 73.52 kDa 
• Atom Count: 5,798 
• Modeled Residue Count: 660 
• Deposited Residue Count: 684 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxythreonine-4-phosphate dehydrogenase	A, B	342	Paraburkholderia phymatum STM815	Mutation(s): 0  Gene Names: pdxA EC: 1.1.1.262
UniProt
Find proteins for B2JVC5 (Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815)) Explore B2JVC5  Go to UniProtKB:  B2JVC5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	E [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.174 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34JQP

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.98	α = 90
b = 99.28	β = 93.92
c = 71.03	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-17 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2013-04-17
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description