8WL1 | pdb_00008wl1

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 (Depositor), 0.257 (DCC)
R-Value Work:
0.216 (Depositor), 0.223 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8WL1

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
Modeled Residue Count: 309
Deposited Residue Count: 312
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.254 (Depositor), 0.257 (DCC)
R-Value Work: 0.216 (Depositor), 0.223 (DCC)
R-Value Observed: 0.218 (Depositor)

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

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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

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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.