3KUU

Structure of the PurE Phosphoribosylaminoimidazole Carboxylase Catalytic Subunit from Yersinia pestis

PDB DOI: https://doi.org/10.2210/pdb3KUU/pdb

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

Deposited: 2009-11-27 Released: 2009-12-22
Deposition Author(s): Anderson, S.M., Wawrzak, Z., Brunzelle, J.S., Onopriyenko, O., Kwon, K., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free: 0.167
R-Value Work: 0.150
R-Value Observed: 0.151

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structure of the PurE Phosphoribosylaminoimidazole Carboxylase Catalytic Subunit from Yersinia pestis

Anderson, S.M., Wawrzak, Z., Brunzelle, J.S., Onopriyenko, O., Kwon, K., Edwards, A., Savchenko, A., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 74.32 kDa
Atom Count: 5,992
Modelled Residue Count: 663
Deposited Residue Count: 696
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylaminoimidazole carboxylase catalytic subunit PurE	A, B, C, D	174	Yersinia pestis	Mutation(s): 1 Gene Names: purE, YPO3076, YP_0848, y1103 EC: 4.1.1.21 (PDB Primary Data), 5.4.99.18 (UniProt)
UniProt
Find proteins for A0A2S9PDM1 (Yersinia pestis) Explore A0A2S9PDM1 Go to UniProtKB: A0A2S9PDM1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2S9PDM1
Sequence Annotations 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 E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth B] E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth C], M [auth C], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free: 0.167
R-Value Work: 0.150
R-Value Observed: 0.151
Space Group: I 4 2 2
Diffraction Data: https://doi.org/10.18430/m33kuu

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.04	α = 90
b = 114.04	β = 90
c = 231.74	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BLU-MAX	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing