6J9U

Complex structure of Lactobacillus casei lactate dehydrogenase penta mutant with pyruvate


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 

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-lactate dehydrogenase
A, B, C, D, E
A, B, C, D, E, F
326Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393Mutation(s): 5 
Gene Names: ldhLBCZ_2323
EC: 1.1.1.27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
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
PYR
Query on PYR

Download Ideal Coordinates CCD File 
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 = 165.32α = 90
b = 82.8β = 91.52
c = 180.15γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

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