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

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
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wwPDB Validation 3D Report Full Report

Validation slider image for 9JLO

This is version 1.0 of the entry. See complete history.

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4L2V5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth B] F [auth B] G [auth B] 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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Shirokova, A.A.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.