4Z1O | pdb_00004z1o

Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from Sulfolobus solfataricus in complex with alpha-phosphoribosylpyrophosphoric acid (PRPP) and Magnesium

• PDB DOI: https://doi.org/10.2210/pdb4Z1O/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharolobus solfataricus 98/2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-27 Released: 2015-04-29 
• Deposition Author(s): Christoffersen, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from Sulfolobus solfataricus in complex with alpha-phosphoribosylpyrophosphoric acid (PRPP) and Magnesium

Christoffersen, S., Hansen, M.R., Jensen, K.S., Larsen, S., Jensen, K.F.

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: 42.19 kDa 
• Atom Count: 3,235 
• Modeled Residue Count: 347 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosyltransferase	A, B	179	Saccharolobus solfataricus 98/2	Mutation(s): 0  Gene Names: GpT-2 EC: 2.4.2.8
UniProt
Find proteins for D0KMY9 (Saccharolobus solfataricus (strain 98/2)) Explore D0KMY9  Go to UniProtKB:  D0KMY9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRP	C [auth A], E [auth B]	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose C5 H13 O14 P3 PQGCEDQWHSBAJP-TXICZTDVSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.784	α = 90
b = 73.784	β = 90
c = 142.906	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
XSCALE	data scaling
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-29 
Deposition Author(s): Christoffersen, S.

Revision History  

• Version 1.0: 2015-04-29
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary