8WL3 | pdb_00008wl3

The structure of D-mandelate dehydrogenase with L243W mutation

PDB DOI: https://doi.org/10.2210/pdb8WL3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Levilactobacillus brevis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

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: 2.00 Å
R-Value Free:
0.251 (Depositor), 0.260 (DCC)
R-Value Work:
0.213 (Depositor), 0.224 (DCC)
R-Value Observed:
0.215 (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

The structure of D-mandelate dehydrogenase with L243W mutation

Liu, F., Rao, Z.M.

To be published.

Macromolecule Content

Total Structure Weight: 66.83 kDa
Atom Count: 4,945
Modeled Residue Count: 623
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydropantoate 2-reductase	A, B	312	Levilactobacillus brevis	Mutation(s): 1 Gene Names: CNR30_12720, UCCLB556_2064, LbMDH EC: 1.1.1.169
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.251 (Depositor), 0.260 (DCC)
R-Value Work: 0.213 (Depositor), 0.224 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.54	α = 90
b = 130.91	β = 92.58
c = 58.09	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	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.