3H3J | pdb_00003h3j

Crystal structure of lactate dehydrogenase mutant (A85R) from staphylococcus aureus complexed with NAD and pyruvate

• PDB DOI: https://doi.org/10.2210/pdb3H3J/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Staphylococcus aureus subsp. aureus COL
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-04-16 Released: 2010-04-28 
• Deposition Author(s): Ho, M.-C., Almo, S.C., Schramm, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.243 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of lactate dehydrogenase mutant (A85R) from staphylococcus aureus complexed with NAD and pyruvate

Ho, M.-C., 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 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 71.1 kDa 
• Atom Count: 5,239 
• Modeled Residue Count: 627 
• 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): 1  Gene Names: ldh1, SACOL0222 EC: 1.1.1.27
UniProt
Find proteins for Q5HJD7 (Staphylococcus aureus (strain COL)) Explore Q5HJD7  Go to UniProtKB:  Q5HJD7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
GOL	E [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
PYR	D [auth A], G [auth B]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.243 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.917	α = 90
b = 122.12	β = 116.2
c = 74.319	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-28 
Deposition Author(s): Ho, M.-C., Almo, S.C., Schramm, V.L.

Revision History  

• Version 1.0: 2010-04-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection