9JLO | pdb_00009jlo

Crystal structure L-lactate dehydrogenase from Lactobacillus reuteri in its apoform

• PDB DOI: https://doi.org/10.2210/pdb9JLO/pdb

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


• Deposited: 2024-09-19 Released: 2025-04-02 
• Deposition Author(s): Matyuta, I.O., Minyaev, M.E., Shirokova, A.A., Pometun, A.A., Tishkov, V.I., Popov, V.O., Boyko, K.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.283 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

Novel extremely stable and active lactate dehydrogenase from l reuteri: structure-function studies and promising usage as an agent against pathogenic biofilms

Pometun, A.A., Shirokova, A.A., Boyko, K.M., Matyuta, I.O., Shaposhnikov, L.A., Atroshenko, D.L., Pometun, E.V., Ageevets, V., Kleimenov, S.Y., Popov, V.O., Tishkov, V.I.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 68.64 kDa 
• Atom Count: 4,794 
• Modeled Residue Count: 629 
• Deposited Residue Count: 638 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase	A, B	319	Limosilactobacillus reuteri	Mutation(s): 0  Gene Names: ldh, B1A73_02515, lr1918 EC: 1.1.1.27
UniProt
Find proteins for A4L2V5 (Limosilactobacillus reuteri) Explore A4L2V5  Go to UniProtKB:  A4L2V5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.283 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.521	α = 90
b = 93.124	β = 90
c = 101.517	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
CrysalisPro	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Matyuta, I.O., Minyaev, M.E., Shirokova, A.A., Pometun, A.A., Tishkov, V.I., Popov, V.O., Boyko, K.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release