6IE0

X-ray crystal structure of 2R,3R-butanediol dehydrogenase from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb6IE0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2018-09-12 Released: 2019-09-18
Deposition Author(s): Wang, X.F., Feng, Y.B., Ji, F.L.
Funding Organization(s): National Science Foundation (China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free: 0.228
R-Value Work: 0.172
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

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

Literature

X-ray crystal structure of 2R,3R-butanediol dehydrogenase from Bacillus subtilis

Wang, X.F., Feng, Y.B., Ji, F.L.

To be published.

Macromolecule Content

Total Structure Weight: 150.15 kDa
Atom Count: 10,552
Modelled Residue Count: 1,388
Deposited Residue Count: 1,388
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(R,R)-butanediol dehydrogenase	A, B, C, D	347	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 EC: 1.1.1.4
UniProt
Find proteins for O34788 (Bacillus subtilis (strain 168)) Explore O34788 Go to UniProtKB: O34788
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O34788
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free: 0.228
R-Value Work: 0.172
R-Value Observed: 0.175
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.839	α = 90
b = 200.839	β = 90
c = 83.266	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-09-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (China)	China	21506025

Revision History (Full details and data files)

Version 1.0: 2019-09-18
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.