8DV0 | pdb_00008dv0

Crystal Structure of a Dephospho-CoA kinase from Rickettsia felis

• PDB DOI: https://doi.org/10.2210/pdb8DV0/pdb

• Classification: TRANSFERASE
• Organism(s): Rickettsia felis URRWXCal2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-07-27 Released: 2022-09-28 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a Dephospho-CoA kinase from Rickettsia felis

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 23.46 kDa 
• Atom Count: 1,815 
• Modeled Residue Count: 192 
• Deposited Residue Count: 199 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dephospho-CoA kinase	A	199	Rickettsia felis URRWXCal2	Mutation(s): 0  Gene Names: coaE, RF_0177 EC: 2.7.1.24
UniProt
Find proteins for Q4UN30 (Rickettsia felis (strain ATCC VR-1525 / URRWXCal2)) Explore Q4UN30  Go to UniProtKB:  Q4UN30

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.13	α = 107.05
b = 39.68	β = 106.87
c = 42.85	γ = 108.3

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MR-Rosetta	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-28 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2022-09-28
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description