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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.264 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Structure based functional analysis of Staphylococcal Phosphoglycerate kinase

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.264 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (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

Entry History 

Deposition Data

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

Revision History  

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