3PQF | pdb_00003pqf

Crystal structure of L-lactate dehydrogenase from Bacillus subtilis mutation H171C complexed with NAD+

PDB DOI: https://doi.org/10.2210/pdb3PQF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-11-26 Released: 2012-01-11
Deposition Author(s): Zhang, Y., Garavito, R.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.235 (Depositor), 0.230 (DCC)
R-Value Work:
0.189 (Depositor), 0.180 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of L-lactate dehydrogenase from Bacillus subtilis mutation H171C complexed with NAD+

zhang, Y., Garavito, R.M.

To be published.

Macromolecule Content

Total Structure Weight: 143.87 kDa
Atom Count: 9,867
Modeled Residue Count: 1,252
Deposited Residue Count: 1,304
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase	A, B, C, D	326	Bacillus subtilis	Mutation(s): 1 Gene Names: ldh, lctE, BSU03050 EC: 1.1.1.27
UniProt
Find proteins for P13714 (Bacillus subtilis (strain 168)) Explore P13714 Go to UniProtKB: P13714
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13714
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain E [auth C] MOL2 format, chain F [auth D] MOL2 format, chain E [auth C] mmCIF format, chain F [auth D] mmCIF format, chain E [auth C]	E [auth C], F [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth C] Focus chain F [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.235 (Depositor), 0.230 (DCC)
R-Value Work: 0.189 (Depositor), 0.180 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.431	α = 90
b = 133.431	β = 90
c = 99.088	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-01-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-01-11
Type: Initial release
Version 1.1: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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.