6IH3

Crystal structure of Phosphite Dehydrogenase from Ralstonia sp. 4506 in complex with non-natural cofactor Nicotinamide Cytosine Dinucleotide

PDB DOI: https://doi.org/10.2210/pdb6IH3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Ralstonia sp. 4506
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.202
R-Value Work: 0.167
R-Value Observed: 0.169

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 73.9 kDa
Atom Count: 5,869
Modelled Residue Count: 658
Deposited Residue Count: 672
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphite dehydrogenase	A, B	336	Ralstonia sp. 4506	Mutation(s): 0 Gene Names: ptxD
UniProt
Find proteins for G4XDR8 (Ralstonia sp. 4506) Explore G4XDR8 Go to UniProtKB: G4XDR8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G4XDR8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A7R Query on A7R Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	[[(2S,3S,4R,5S)-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3S,4R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate C₂₀ H₂₈ N₅ O₁₅ P₂ CRWNYXSXULHVKY-JKHXZYGESA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.202
R-Value Work: 0.167
R-Value Observed: 0.169
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.77	α = 90
b = 122.584	β = 90
c = 61.662	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-03-13

Deposition Author(s):

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.