9BKZ | pdb_00009bkz

Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (CoA and ADP bound)

• PDB DOI: https://doi.org/10.2210/pdb9BKZ/pdb

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


• Deposited: 2024-04-29 Released: 2024-05-08 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, 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: 2.35 Å
• R-Value Free: 
  0.283 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (CoA and ADP bound)

Liu, L., Lovell, S., Battaile, K.P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 49.44 kDa 
• Atom Count: 3,148 
• Modeled Residue Count: 396 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dephospho-CoA kinase	A, B	214	Klebsiella aerogenes	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
COA (Subject of Investigation/LOI)	D [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
ADP (Subject of Investigation/LOI)	C [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MPD	E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.283 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m39bkz

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.096	α = 90
b = 50.551	β = 115.22
c = 70.595	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: 2024-05-08 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, 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	S10OD030394

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release