4RQA | pdb_00004rqa

Crystal Structure of a Hypoxanthine Phosphoribosyltransferase (target ID NYSGRC-029686) from Staphylococcus aureus (orthorhombic space group)

• PDB DOI: https://doi.org/10.2210/pdb4RQA/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus subsp. aureus USA300_TCH1516
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-31 Released: 2014-11-26 
• Deposition Author(s): Ghosh, A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.194 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Literature

Crystal Structure of a Hypoxanthine Phosphoribosyltransferase (target ID NYSGRC-029686) from Staphylococcus aureus (orthorhombic space group)

Ghosh, A., Ahmed, A., Bhoshle, R., Seidel, R., Stead, M., Toro, R., Schramm, V.L., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.61 kDa 
• Atom Count: 1,544 
• Modeled Residue Count: 176 
• Deposited Residue Count: 186 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypoxanthine phosphoribosyltransferase	A	186	Staphylococcus aureus subsp. aureus USA300_TCH1516	Mutation(s): 0  Gene Names: hpt EC: 2.4.2.8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.194 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.158	α = 90
b = 71.919	β = 90
c = 103.036	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction
HKL2Map	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-26 
Deposition Author(s): Ghosh, A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary