6J9T | pdb_00006j9t

Complex structure of Lactobacillus casei lactate dehydrogenase with fructose-1,6-bisphosphate

• PDB DOI: https://doi.org/10.2210/pdb6J9T/pdb
• Entry: 6J9T supersedes: 3VKV

• Classification: OXIDOREDUCTASE
• Organism(s): Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.226 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

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: 215.02 kDa 
• Atom Count: 14,571 
• Modeled Residue Count: 1,875 
• 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): 0  Gene Names: ldh, LBCZ_2323 EC: 1.1.1.27
UniProt
Find proteins for P00343 (Lacticaseibacillus casei) Explore P00343  Go to UniProtKB:  P00343

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FBP	I [auth B], M [auth E], O [auth F]	1,6-di-O-phosphono-beta-D-fructofuranose C6 H14 O12 P2 RNBGYGVWRKECFJ-ARQDHWQXSA-N
SO4	G [auth A], H [auth B], J [auth C], K [auth D], L [auth E], N [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.226 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.25	α = 90
b = 83.582	β = 91.53
c = 180.094	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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: 3VKV

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary