4FUR | pdb_00004fur

Crystal Structure of Urease subunit gamma 2 from Brucella melitensis biovar Abortus 2308

PDB DOI: https://doi.org/10.2210/pdb4FUR/pdb

Classification: HYDROLASE
Organism(s): Brucella abortus 2308
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-06-28 Released: 2012-08-15
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.188 (Depositor), 0.210 (DCC)
R-Value Work:
0.151 (Depositor), 0.170 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Urease subunit gamma 2 from Brucella melitensis biovar Abortus 2308

Fairman, J.W., Davies, D.R., Staker, B.L., Stewart, L.

To be published.

Macromolecule Content

Total Structure Weight: 68.06 kDa
Atom Count: 5,078
Modeled Residue Count: 598
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urease subunit gamma 2	A, B, C, D, E A, B, C, D, E, F	104	Brucella abortus 2308	Mutation(s): 0 Gene Names: ureA2, BAB1_1376 EC: 3.5.1.5
UniProt
Find proteins for Q2YQE0 (Brucella abortus (strain 2308)) Explore Q2YQE0 Go to UniProtKB: Q2YQE0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2YQE0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain T [auth F] MOL2 format, chain T [auth F] mmCIF format, chain T [auth F]	T [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain T [auth F] Interactions & Density Focus chain T [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth E] SDF format, chain P [auth E] SDF format, chain Q [auth F] SDF format, chain R [auth F] SDF format, chain S [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth F] MOL2 format, chain S [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth E] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth F] mmCIF format, chain S [auth F]	G [auth A] H [auth A] I [auth A] J [auth B] K [auth C] G [auth A], H [auth A], I [auth A], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D], O [auth E], P [auth E], Q [auth F], R [auth F], S [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.188 (Depositor), 0.210 (DCC)
R-Value Work: 0.151 (Depositor), 0.170 (DCC)
R-Value Observed: 0.153 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34FUR

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.51	α = 90
b = 145.01	β = 90
c = 137.18	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-08-15

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2012-08-15
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description