6KP5 | pdb_00006kp5

crystal structure of Xanthine-guanine phosphoribosyltransferase (XGPRT) from Yersinia pestis in P21212 space group with sulphate ions in the active site

• PDB DOI: https://doi.org/10.2210/pdb6KP5/pdb

• Classification: TRANSFERASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-08-14 Released: 2019-09-25 
• Deposition Author(s): Lankipalli, S., Ramagopal, U.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.186 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

crystal structure of Xanthine-guanine phosphoribosyltransferase (XGPRT) from Yersinia pestis in P21212 space group

Lankipalli, S., Ramagopal, U.A.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.53 kDa 
• Atom Count: 2,493 
• Modeled Residue Count: 277 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xanthine phosphoribosyltransferase	A, B	153	Yersinia pestis	Mutation(s): 0  Gene Names: gpt, YPO3225, y0963, YP_0708 EC: 2.4.2.22 (PDB Primary Data), 2.4.2 (UniProt)
UniProt
Find proteins for Q8ZC05 (Yersinia pestis) Explore Q8ZC05  Go to UniProtKB:  Q8ZC05

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.186 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.32	α = 90
b = 94.63	β = 90
c = 51.67	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-25 
Deposition Author(s): Lankipalli, S., Ramagopal, U.A.

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description