6J9U | pdb_00006j9u

Complex structure of Lactobacillus casei lactate dehydrogenase penta mutant with pyruvate

PDB DOI: https://doi.org/10.2210/pdb6J9U/pdb
Entry: 6J9U supersedes: 3VPF

Classification: OXIDOREDUCTASE
Organism(s): Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-01-24 Released: 2019-02-06
Deposition Author(s): Arai, K., Miyanaga, A., Uchikoba, H., Fushinobu, S., Taguchi, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free:
0.227 (Depositor), 0.229 (DCC)
R-Value Work:
0.191 (Depositor), 0.197 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of penta mutant of L-lactate dehydrogenase from Lactobacillus casei

Arai, K., Miyanaga, A., Uchikoba, H., Fushinobu, S., Taguchi, H.

To be published.

Macromolecule Content

Total Structure Weight: 215.15 kDa
Atom Count: 14,596
Modeled Residue Count: 1,882
Deposited Residue Count: 1,956
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase	A, B, C, D, E A, B, C, D, E, F	326	Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393	Mutation(s): 5 Gene Names: ldh, LBCZ_2323 EC: 1.1.1.27
UniProt
Find proteins for P00343 (Lacticaseibacillus casei) Explore P00343 Go to UniProtKB: P00343
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00343
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain Q [auth F] SDF format, chain P [auth E] SDF format, chain O [auth E] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth F] MOL2 format, chain P [auth E] MOL2 format, chain O [auth E] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth F] mmCIF format, chain P [auth E] mmCIF format, chain O [auth E] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A]	H [auth A] I [auth B] J [auth B] L [auth C] N [auth D] H [auth A], I [auth B], J [auth B], L [auth C], N [auth D], O [auth E], P [auth E], Q [auth F], R [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F]
PYR Query on PYR Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain G [auth A] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain G [auth A] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain G [auth A]	G [auth A], K [auth C], M [auth D]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth C] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.227 (Depositor), 0.229 (DCC)
R-Value Work: 0.191 (Depositor), 0.197 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.32	α = 90
b = 82.8	β = 91.52
c = 180.15	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-02-06

Deposition Author(s):

This entry supersedes: 3VPF

Revision History (Full details and data files)

Version 1.0: 2019-02-06
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Refinement description
Version 2.1: 2023-11-22
Changes: Refinement description