4DG5 | pdb_00004dg5

Crystal structure of staphylococcal Phosphoglycerate kinase

PDB DOI: https://doi.org/10.2210/pdb4DG5/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus subsp. aureus MRSA252
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-01-25 Released: 2013-01-30
Deposition Author(s): Roychowdhury, A., Mukherjee, S., Dutta, D., Das, A.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.264 (Depositor), 0.268 (DCC)
R-Value Work:
0.172 (Depositor), 0.174 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structure based functional analysis of Staphylococcal Phosphoglycerate kinase

Roychowdhury, A., Mukherjee, S., Dutta, D., Das, A.K.

To be published.

Macromolecule Content

Total Structure Weight: 43.5 kDa
Atom Count: 3,259
Modeled Residue Count: 395
Deposited Residue Count: 403
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate kinase	A	403	Staphylococcus aureus subsp. aureus MRSA252	Mutation(s): 0 Gene Names: pgk, SAR0829 EC: 2.7.2.3
UniProt
Find proteins for Q6GIL7 (Staphylococcus aureus (strain MRSA252)) Explore Q6GIL7 Go to UniProtKB: Q6GIL7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6GIL7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.264 (Depositor), 0.268 (DCC)
R-Value Work: 0.172 (Depositor), 0.174 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.137	α = 90
b = 74.748	β = 95.72
c = 58.665	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-01-30

Deposition Author(s):

Roychowdhury, A.

Revision History (Full details and data files)

Version 1.0: 2013-01-30
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

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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.