8G0T | pdb_00008g0t

Crystal Structure of Acetyl-CoA synthetase in complex with a cyclopropyl ester AMP inhibitor from Cryptococcus neoformans H99

• PDB DOI: https://doi.org/10.2210/pdb8G0T/pdb

• Classification: LIGASE
• Organism(s): Cryptococcus neoformans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-02-01 Released: 2023-02-15 
• 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: 2.45 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Acetyl-CoA synthetase in complex with a cyclopropyl ester AMP inhibitor from Cryptococcus neoformans H99

Liu, L., Lovell, S., Battaile, K.P., Staker, B.L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 233.78 kDa 
• Atom Count: 15,462 
• Modeled Residue Count: 1,971 
• Deposited Residue Count: 2,082 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-coenzyme A synthetase	A, B, C	694	Cryptococcus neoformans	Mutation(s): 0  EC: 6.2.1.1
UniProt
Find proteins for J9VFT1 (Cryptococcus neoformans (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)) Explore J9VFT1  Go to UniProtKB:  J9VFT1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YHK (Subject of Investigation/LOI)	F [auth A], H [auth B], I [auth C]	5'-O-[(R)-(cyclopropyloxy)(hydroxy)phosphoryl]adenosine C13 H18 N5 O7 P FJCZQSQASCNEEZ-QYVSTXNMSA-N
EDO	D [auth A], E [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38G0T

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.682	α = 113.29
b = 84.785	β = 106.9
c = 105.471	γ = 90.96

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: 2023-02-15 
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	OD030394

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection