3PQD | pdb_00003pqd

Crystal structure of L-lactate dehydrogenase from Bacillus subtilis complexed with FBP and NAD+

• PDB DOI: https://doi.org/10.2210/pdb3PQD/pdb

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


• Deposited: 2010-11-26 Released: 2012-01-18 
• Deposition Author(s): Zhang, Y., Garavito, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.269 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

Crystal structure of L-lactate dehydrogenase from Bacillus subtilis complexed with FBP and NAD+

zhang, Y., Garavito, R.M.

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 and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 287.39 kDa 
• Atom Count: 19,005 
• Modeled Residue Count: 2,449 
• Deposited Residue Count: 2,608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase	A, B, C, D, E, F, G, H	326	Bacillus subtilis	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	J [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
FBP	I [auth C], K [auth D], L [auth F], M [auth G]	1,6-di-O-phosphono-beta-D-fructofuranose C6 H14 O12 P2 RNBGYGVWRKECFJ-ARQDHWQXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.269 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.041	α = 90
b = 171.041	β = 90
c = 96.272	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

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): Zhang, Y., Garavito, R.M.

Revision History  

• Version 1.0: 2012-01-18
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Structure summary