8I83 | pdb_00008i83

Crystal Structure of phosphinothricin dehydrogenase

PDB DOI: https://doi.org/10.2210/pdb8I83/pdb

Classification: OXIDOREDUCTASE
Organism(s): Lysinibacillus composti
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-02-03 Released: 2024-02-14
Deposition Author(s): Cheng, F., Xue, Y.P., Zheng, Y.G., Zou, S.P.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free:
0.250 (Depositor), 0.250 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of phosphinothricin dehydrogenase

Cheng, F., Xue, Y.P., Zheng, Y.G.

To be published.

Macromolecule Content

Total Structure Weight: 280.86 kDa
Atom Count: 18,861
Modeled Residue Count: 2,378
Deposited Residue Count: 2,532
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase	A B C D E [auth F] A, B, C, D, E [auth F], F [auth E]	422	Lysinibacillus composti	Mutation(s): 0 Gene Names: EBB45_13425
UniProt
Find proteins for A0A3N9UCW8 (Lysinibacillus composti) Explore A0A3N9UCW8 Go to UniProtKB: A0A3N9UCW8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3N9UCW8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth F] MOL2 format, chain G [auth F] mmCIF format, chain G [auth F]	G [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth F] Interactions & Density Focus chain G [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.250 (Depositor), 0.250 (DCC)
R-Value Work: 0.198 (Depositor), 0.200 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.13	α = 90
b = 126.667	β = 90
c = 223.741	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31970046

Revision History (Full details and data files)

Version 1.0: 2024-02-14
Type: Initial release

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 R01GM157729.