5ER6 | pdb_00005er6

Crystal structure of an oxidoreductase from Brucella ovis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.167 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.146 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of a short-chain dehydrogenase from Brucella ovis with apo and coenzyme NAD + -bound protomer chains.

Zupko, S.P.Konstanty, A.T.Mayclin, S.J.Choi, R.Serbzhinskiy, D.Robles, E.Moses, V.Barrett, L.K.Van Voorhis, W.C.Edwards, T.E.Myler, P.J.Torelli, A.T.French, J.B.Hicks, K.A.

(2025) Acta Crystallogr F Struct Biol Commun 

  • DOI: https://doi.org/10.1107/S2053230X25009227
  • Primary Citation of Related Structures:  
    5ER6, 5HA5

  • PubMed Abstract: 

    Short-chain dehydrogenases (SDRs) are a family of NAD(P)-dependent enzymes involved in redox reactions, specifically carbonyl-alcohol reductions. Here, we report the apo and NAD + -bound structures of an SDR from the pathogenic organism Brucella ovis. B. ovis primarily affects sheep and other livestock, resulting in reduced fertility. Based on sequence and structural alignment, the B. ovis SDR (BoSDR) is a classical SDR. Classical SDRs have a canonical YxxxK active-site sequence in which the catalytic general base is a tyrosine residue located at position 163. In addition, the putative active site also contains a serine residue (Ser150) and lysine residue (Lys167) that are hypothesized to be involved in catalysis. BoSDR is a biological and crystallographic tetramer. In the coenzyme-bound structure, two different orientations of the NAD + coenzyme are fortuitously observed, which provides insights into the conformational changes that accompany coenzyme binding. The apo and NAD + -bound structures provide valuable information about the unique structural features of enzymes in the SDR superfamily.


  • Organizational Affiliation
    • Department of Chemistry, State University of New York at Cortland, Cortland, NY 13045, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxidoreductase, short chain dehydrogenase/reductase family
A, B, C, D
251Brucella ovis ATCC 25840Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3ATY4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
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
ACT
Query on ACT

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.167 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.146 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.01α = 90
b = 94.81β = 99.54
c = 99.49γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Cootmodel building
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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
  • Version 1.2: 2025-12-10
    Changes: Database references, Structure summary