6J9U

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 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

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.

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

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: 215.15 kDa 
• Atom Count: 14,596 
• Modelled Residue Count: 1,882 
• Deposited Residue Count: 1,956 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	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
PYR	G [auth A], K [auth C], M [auth D]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.227 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• 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

Entry History 

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Arai, K., Miyanaga, A., Uchikoba, H., Fushinobu, S., Taguchi, H.
• This entry supersedes: 3VPF

Revision History  

• 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