6IH8 | pdb_00006ih8

Crystal structure of Phosphite Dehydrogenase mutant I151R/P176R/M207A from Ralstonia sp. 4506

• PDB DOI: https://doi.org/10.2210/pdb6IH8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Ralstonia sp. 4506
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-09-28 Released: 2019-03-13 
• Deposition Author(s): Song, X., Feng, Y., Liu, Y., Zhao, Z.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Structural Insights into Phosphite Dehydrogenase Variants Favoring a Non-natural Redox Cofactor

Liu, Y., Feng, Y., Wang, L., Guo, X., Liu, W., Li, Q., Wang, X., Xue, S., Zhao, Z.

(2019) ACS Catal 9: 1883-1887

• DOI: https://doi.org/10.1021/acscatal.8b04822

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 147.65 kDa 
• Atom Count: 10,702 
• Modeled Residue Count: 1,314 
• Deposited Residue Count: 1,352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphite dehydrogenase	A, B, C, D	338	Ralstonia sp. 4506	Mutation(s): 3  Gene Names: ptxD
UniProt
Find proteins for G4XDR8 (Ralstonia sp. 4506) Explore G4XDR8  Go to UniProtKB:  G4XDR8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.03	α = 90
b = 118.591	β = 90.65
c = 98.228	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-13 
Deposition Author(s): Song, X., Feng, Y., Liu, Y., Zhao, Z.

Revision History  

• Version 1.0: 2019-03-13
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description