4XKJ | pdb_00004xkj

a Novel D-lactate Dehydrogenase from Sporolactobacillus sp

• PDB DOI: https://doi.org/10.2210/pdb4XKJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sporolactobacillus inulinus CASD
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-01-12 Released: 2015-08-05 
• Deposition Author(s): Bo, Y., Hui, D., Xiang, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

a Novel D-lactate Dehydrogenase from Sporolactobacillus sp

Bo, Y., Hui, D., Xiang, L.

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: 74.91 kDa 
• Atom Count: 5,200 
• Modeled Residue Count: 664 
• Deposited Residue Count: 670 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-lactate dehydrogenase	A, B	335	Sporolactobacillus inulinus CASD	Mutation(s): 0
UniProt
Find proteins for A0A0M3KL04 (Sporolactobacillus inulinus CASD) Explore A0A0M3KL04  Go to UniProtKB:  A0A0M3KL04

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.263	α = 90
b = 109.505	β = 90
c = 113.003	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-05 
Deposition Author(s): Bo, Y., Hui, D., Xiang, L.

Revision History  

• Version 1.0: 2015-08-05
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description