3D0O | pdb_00003d0o

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.203 (Depositor), 0.202 (DCC)
R-Value Work:
0.170 (Depositor), 0.171 (DCC)
R-Value Observed:
0.172 (Depositor)

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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Lactate Dehydrogenase from Staphylococcus Aureus

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

To be published.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5HJD7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.203 (Depositor), 0.202 (DCC)
R-Value Work: 0.170 (Depositor), 0.171 (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

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Entry History

Deposition Data

Released Date: 2009-05-12

Deposition Author(s):

Gutierrez, J.A.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.