3WX0 | pdb_00003wx0

The crystal structure of D-lactate dehydrogenase from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb3WX0/pdb

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


• Deposited: 2014-07-08 Released: 2015-07-08 
• Deposition Author(s): Furukawa, N., Togawa, M., Miyanaga, A., Nakajima, M., Taguchi, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.271 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Allosteric D-lactate dehydrogenases from three Gram-negative bacteria

Furukawa, N., Togawa, M., Miyanaga, A., Nakajima, M., Taguchi, H.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 154.38 kDa 
• Atom Count: 8,746 
• Modeled Residue Count: 1,128 
• Deposited Residue Count: 1,380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding	A, B, C, D	345	Escherichia coli BL21(DE3)	Mutation(s): 0  Gene Names: B21_01364, ECBD_2243, ECD_01352, ldhA EC: 1.1.1.28

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.271 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.029	α = 90
b = 131.029	β = 90
c = 405.746	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-08 
Deposition Author(s): Furukawa, N., Togawa, M., Miyanaga, A., Nakajima, M., Taguchi, H.

Revision History  

• Version 1.0: 2015-07-08
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description