4KMS | pdb_00004kms

Crystal structure of Acetoacetyl-CoA reductase from Rickettsia felis

• PDB DOI: https://doi.org/10.2210/pdb4KMS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rickettsia felis Marseille-URRWFXCal2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-05-08 Released: 2013-05-22 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Lukacs, C., Edwards, T.E., Lorimer, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.210 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of acetoacetyl-CoA reductase from Rickettsia felis.

Rodarte, J.V., Abendroth, J., Edwards, T.E., Lorimer, D.D., Staker, B.L., Zhang, S., Myler, P.J., McLaughlin, K.J.

(2021) Acta Crystallogr F Struct Biol Commun 77: 54-60

• PubMed: 33620038 
• DOI: https://doi.org/10.1107/S2053230X21001497
• Primary Citation Related Structures: 
  4KMS, 7MI0


• PubMed Abstract: 
  

  Rickettsia felis, a Gram-negative bacterium that causes spotted fever, is of increasing interest as an emerging human pathogen. R. felis and several other Rickettsia strains are classed as National Institute of Allergy and Infectious Diseases priority pathogens. In recent years, R. felis has been shown to be adaptable to a wide range of hosts, and many fevers of unknown origin are now being attributed to this infectious agent. Here, the structure of acetoacetyl-CoA reductase from R. felis is reported at a resolution of 2.0 Å. While R. felis acetoacetyl-CoA reductase shares less than 50% sequence identity with its closest homologs, it adopts a fold common to other short-chain dehydrogenase/reductase (SDR) family members, such as the fatty-acid synthesis II enzyme FabG from the prominent pathogens Staphylococcus aureus and Bacillus anthracis. Continued characterization of the Rickettsia proteome may prove to be an effective means of finding new avenues of treatment through comparative structural studies.

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Organizational Affiliation: 
• Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, New York, USA.
Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA.

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)

Macromolecule Content 

• Total Structure Weight: 54.62 kDa 
• Atom Count: 3,768 
• Modeled Residue Count: 462 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetoacetyl-CoA reductase	A, B	249	Rickettsia felis Marseille-URRWFXCal2	Mutation(s): 0  Gene Names: phbB, RF_015, RF_0153 EC: 1.1.1.100
UniProt
Find proteins for Q4UN54 (Rickettsia felis (strain ATCC VR-1525 / URRWXCal2)) Explore Q4UN54  Go to UniProtKB:  Q4UN54

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.210 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34KMS

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.11	α = 90
b = 99.7	β = 90
c = 73.37	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-22 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Lukacs, C., Edwards, T.E., Lorimer, D.

Revision History  

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2021-03-10
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description