8GBB | pdb_00008gbb

Short-chain dehydrogenase/reductase (SDR) from multi-drug resistant Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb8GBB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-02-24 Released: 2023-05-10 
• Deposition Author(s): Shaw, K.I., Ghafoori, S.M., Forwood, J.K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystallographic structure determination and analysis of a potential short-chain dehydrogenase/reductase (SDR) from multi-drug resistant Acinetobacter baumannii.

Ghafoori, S.M., Abdollahpour, S., Shirmast, P., Forwood, J.K.

(2023) PLoS One 18: e0289992-e0289992

• PubMed: 37616198 
• DOI: https://doi.org/10.1371/journal.pone.0289992
• Primary Citation Related Structures: 
  8GBB


• PubMed Abstract: 
  

  Bacterial antibiotic resistance remains an ever-increasing worldwide problem, requiring new approaches and enzyme targets. Acinetobacter baumannii is recognised as one of the most significant antibiotic-resistant bacteria, capable of carrying up to 45 different resistance genes, and new drug discovery targets for this organism is an urgent priority. Short-chain dehydrogenase/reductase enzymes are a large protein family with >60,000 members involved in numerous biosynthesis pathways. Here, we determined the structure of an SDR protein from A. baumannii and assessed the putative co-factor comparisons with previously co-crystalised enzymes and cofactors. This study provides a basis for future studies to examine these potential co-factors in vitro.

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Organizational Affiliation: 
• School of Dentistry and Medical Sciences, Charles Sturt University, Wagga, Wagga, NSW, Australia.
Menzies Health Institute Queensland and School of Medical Sciences, Griffith University, Gold Coast, QLD, Australia.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 55.65 kDa 
• Atom Count: 4,043 
• Modeled Residue Count: 520 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SDR family oxidoreductase	A, B	261	Acinetobacter baumannii	Mutation(s): 0  Gene Names: F4T85_19375, FJU42_12090, HBK86_07635 EC: 1.1.1.100
UniProt
Find proteins for A0A0M3FP68 (Acinetobacter baumannii) Explore A0A0M3FP68  Go to UniProtKB:  A0A0M3FP68

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.431	α = 90
b = 109.46	β = 90
c = 136.92	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-10 
Deposition Author(s): Shaw, K.I., Ghafoori, S.M., Forwood, J.K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-05-10
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references