3WX0

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.271
R-Value Work: 0.231
R-Value Observed: 0.233

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Allosteric D-lactate dehydrogenases from three Gram-negative bacteria

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

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
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: 3.30 Å
R-Value Free: 0.271
R-Value Work: 0.231
R-Value Observed: 0.233
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-07-08

Deposition Author(s):

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.