6KQC | pdb_00006kqc

Crystal structure of E136F mutant of Xanthine-guanine phosphoribosyltransferase from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb6KQC/pdb

• Classification: TRANSFERASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-08-16 Released: 2019-09-11 
• Deposition Author(s): Lankipalli, S., Ramagopal, U.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.212 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of E136F mutant of Xanthine-guanine phosphoribosyltransferase from Yersinia pestis

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: 34.38 kDa 
• Atom Count: 2,347 
• Modeled Residue Count: 283 
• 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): 1  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A], D [auth B], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.212 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.38	α = 90
b = 96.65	β = 90
c = 51.029	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Lankipalli, S., Ramagopal, U.A.

Revision History  

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