8WL4 | pdb_00008wl4

The structure of D-mandelate dehydrogenase with L103G and T143G mutations

• PDB DOI: https://doi.org/10.2210/pdb8WL4/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.294 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: experimental

Literature

The structure of D-mandelate dehydrogenase with L103G and T143G mutations

Liu, F., Rao, Z.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.57 kDa 
• Atom Count: 4,738 
• Modeled Residue Count: 624 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydropantoate 2-reductase	A, B	312	Levilactobacillus brevis	Mutation(s): 2  Gene Names: CNR30_12720, UCCLB556_2064, LbMDH EC: 1.1.1.169

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.294 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.62	α = 90
b = 131.99	β = 90
c = 58.64	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Liu, F., Rao, Z.M.

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

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release