5ER6

Crystal structure of an oxidoreductase from Brucella ovis

PDB DOI: https://doi.org/10.2210/pdb5ER6/pdb

Classification: OXIDOREDUCTASE
Organism(s): Brucella ovis ATCC 25840
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-11-13 Released: 2015-11-25
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.167
R-Value Work: 0.146
R-Value Observed: 0.146

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 an oxidoreductase from Brucella ovis

Mayclin, S.J., Abendroth, J., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 103.86 kDa
Atom Count: 8,281
Modelled Residue Count: 969
Deposited Residue Count: 1,004
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, short chain dehydrogenase/reductase family	A, B, C, D	251	Brucella ovis ATCC 25840	Mutation(s): 0 Gene Names: BOV_A0028
UniProt
Find proteins for A0A0H3ATY4 (Brucella ovis (strain ATCC 25840 / 63/290 / NCTC 10512)) Explore A0A0H3ATY4 Go to UniProtKB: A0A0H3ATY4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3ATY4
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 G [auth A] SDF format, chain H [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D]	G [auth A] H [auth B] K [auth B] N [auth C] O [auth C] G [auth A], H [auth B], K [auth B], N [auth C], O [auth C], R [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D]	E [auth A] F [auth A] I [auth B] J [auth B] L [auth C] E [auth A], F [auth A], I [auth B], J [auth B], L [auth C], M [auth C], P [auth D], Q [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.167
R-Value Work: 0.146
R-Value Observed: 0.146
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M35ER6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.01	α = 90
b = 94.81	β = 99.54
c = 99.49	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-11-25

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2015-11-25
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description