2XXB | pdb_00002xxb

Penta-mutant of Thermus thermophilus lactate dehydrogenase, complex with AMP

• PDB DOI: https://doi.org/10.2210/pdb2XXB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): Yes 


• Deposited: 2010-11-09 Released: 2010-11-17 
• Deposition Author(s): Diop, F., Coquelle, N., Vellieux, F.M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.289 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

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

Diop, F., Coquelle, N., 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: 65.89 kDa 
• Atom Count: 4,968 
• Modeled Residue Count: 620 
• Deposited Residue Count: 620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-LACTATE DEHYDROGENASE	A, B	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A], D [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.289 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.99	α = 90
b = 153.47	β = 90
c = 150.61	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: 2010-11-17 
Deposition Author(s): Diop, F., Coquelle, N., Vellieux, F.M.D.

Revision History  

• Version 1.0: 2010-11-17
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-02-28
  Changes: Advisory, Source and taxonomy
• Version 1.4: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.5: 2023-12-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description