8WL1

The crystal structure of D-mandelate dehydrogenase from Lactobacillus brevis

PDB DOI: https://doi.org/10.2210/pdb8WL1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Levilactobacillus brevis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-09-29 Released: 2024-10-02
Deposition Author(s): Liu, F., Rao, Z.M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.254
R-Value Work: 0.216
R-Value Observed: 0.218

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of D-mandelate dehydrogenase from Lactobacillus brevis

Liu, F., Rao, Z.M.

To be published.

Macromolecule Content

Total Structure Weight: 33.34 kDa
Atom Count: 2,477
Modelled Residue Count: 309
Deposited Residue Count: 312
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydropantoate 2-reductase	A	312	Levilactobacillus brevis	Mutation(s): 0 Gene Names: CNR30_12720, UCCLB556_2064, LbMDH EC: 1.1.1.169
UniProt
Find proteins for A0A7Z6MKR0 (Levilactobacillus brevis) Explore A0A7Z6MKR0 Go to UniProtKB: A0A7Z6MKR0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7Z6MKR0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.254
R-Value Work: 0.216
R-Value Observed: 0.218
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.31	α = 90
b = 132	β = 90
c = 59	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171471

Revision History (Full details and data files)

Version 1.0: 2024-10-02
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.