3D0O

Crystal structure of Lactate Dehydrogenase from Staphylococcus Aureus

• PDB DOI: https://doi.org/10.2210/pdb3D0O/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Staphylococcus aureus subsp. aureus COL
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-02 Released: 2009-05-12 
• Deposition Author(s): Ho, M., Gutierrez, J.A., Almo, S.C., Schramm, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

Crystal structure of Lactate Dehydrogenase from Staphylococcus Aureus

Ho, M., Gutierrez, J.A., Almo, S.C., Schramm, V.L.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.24 kDa 
• Atom Count: 5,375 
• Modelled Residue Count: 619 
• Deposited Residue Count: 634 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase 1	A, B	317	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0  Gene Names: ldh1, SACOL0222 EC: 1.1.1.27
UniProt
Find proteins for Q5HJD7 (Staphylococcus aureus (strain COL)) Explore Q5HJD7  Go to UniProtKB:  Q5HJD7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.765	α = 90
b = 74.503	β = 129.07
c = 96.306	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-12 
Deposition Author(s): Ho, M., Gutierrez, J.A., Almo, S.C., Schramm, V.L.

Revision History  

• Version 1.0: 2009-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references