Macromolecule Content

Total Structure Weight: 34.53 kDa
Atom Count: 2493
Residue Count: 277
Unique protein chains: 1

6KP5

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

DOI: 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.186
R-Value Work: 0.162
R-Value Observed: 0.163

wwPDB Validation 3D Report Full Report

Literature

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

Lankipalli, S., Ramagopal, U.A.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

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)
Find proteins for Q8ZC05 (Yersinia pestis) Explore Q8ZC05 Go to UniProtKB: Q8ZC05
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain D [A] SDF format, chain E [B] SDF format, chain F [B] MOL2 format, chain C [A] MOL2 format, chain D [A] MOL2 format, chain E [B] MOL2 format, chain F [B]	A, B	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.186
R-Value Work: 0.162
R-Value Observed: 0.163
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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2019-08-14
Released Date: 2019-09-25

Deposition Author(s):

Ramagopal, U.A.

Revision History

Version 1.0: 2019-09-25
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.