2XXJ | pdb_00002xxj

Penta mutant of lactate dehydrogenase from Thermus thermophilus, ternary complex

• PDB DOI: https://doi.org/10.2210/pdb2XXJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-11-10 Released: 2010-11-24 
• Deposition Author(s): Tickle, J., de Mendoza Barbera, E., Vellieux, F.M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.226 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Lactate Dehydrogenase from T. Thermophilus, Penta- Mutant (Ternary Complex)

Tickle, J., De Mendoza Barbera, E., Vellieux, F.M.D.

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)

Macromolecule Content 

• Total Structure Weight: 132.09 kDa 
• Atom Count: 9,995 
• Modeled Residue Count: 1,239 
• Deposited Residue Count: 1,240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-LACTATE DEHYDROGENASE	A, B, C, D	310	Thermus thermophilus HB8	Mutation(s): 5  EC: 1.1.1.27
UniProt
Find proteins for Q5SJA1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJA1  Go to UniProtKB:  Q5SJA1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	G [auth B], J [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4	E [auth A], H [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
OXM	F [auth B], I [auth D]	OXAMIC ACID C2 H3 N O3 SOWBFZRMHSNYGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.226 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.15	α = 90
b = 147.36	β = 90
c = 152.28	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-24 
Deposition Author(s): Tickle, J., de Mendoza Barbera, E., Vellieux, F.M.D.

Revision History  

• Version 1.0: 2010-11-24
  Type: Initial release
  
• Version 1.1: 2011-08-03
  Changes: Atomic model, Derived calculations, Other, Version format compliance
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description