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), 0.261 (DCC)
R-Value Work:
0.213 (Depositor)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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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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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.251 (Depositor), 0.261 (DCC)
R-Value Work: 0.213 (Depositor)
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

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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.