6IE0 | pdb_00006ie0

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 (Depositor), 0.227 (DCC)
R-Value Work:
0.172 (Depositor), 0.172 (DCC)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

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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
Modeled Residue Count: 1,388
Deposited Residue Count: 1,388
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF 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 (Depositor), 0.227 (DCC)
R-Value Work: 0.172 (Depositor), 0.172 (DCC)
R-Value Observed: 0.175 (Depositor)

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

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.