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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.212 (Depositor), 0.192 (DCC)
R-Value Work:
0.180 (Depositor)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

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

Lankipalli, S., Ramagopal, U.A.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZC05
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.212 (Depositor), 0.192 (DCC)
R-Value Work: 0.180 (Depositor)
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

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Entry History

Deposition Data

Released Date: 2019-09-11

Deposition Author(s):

Ramagopal, U.A.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.