8SBN

Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (P21 Form 1)

• PDB DOI: https://doi.org/10.2210/pdb8SBN/pdb

• Classification: TRANSFERASE
• Organism(s): Klebsiella aerogenes KCTC 2190
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-04-03 Released: 2023-04-12 
• 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), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.166 
• R-Value Work: 0.140 
• R-Value Observed: 0.141 

Starting Model: experimental

Literature

Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (P21 Form 1)

Seibold, S., Lovell, S., Liu, L., Battaile, K.P.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 24.42 kDa 
• Atom Count: 1,978 
• Modelled Residue Count: 201 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dephospho-CoA kinase	A	214	Klebsiella aerogenes KCTC 2190	Mutation(s): 2  Gene Names: coaE, EAE_11320 EC: 2.7.1.24
UniProt
Find proteins for A0A0H3FR62 (Klebsiella aerogenes (strain ATCC 13048 / DSM 30053 / CCUG 1429 / JCM 1235 / KCTC 2190 / NBRC 13534 / NCIMB 10102 / NCTC 10006 / CDC 819-56)) Explore A0A0H3FR62  Go to UniProtKB:  A0A0H3FR62

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEZ	B [auth A], C [auth A], D [auth A]	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.166 
• R-Value Work: 0.140 
• R-Value Observed: 0.141 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M38SBN

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.905	α = 90
b = 48.733	β = 95.42
c = 65.73	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-12 
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	75N93022C00036
National Institutes of Health/Office of the Director	United States	OD030394

Revision History  

• Version 1.0: 2023-04-12
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection