8G0R | pdb_00008g0r

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

• PDB DOI: https://doi.org/10.2210/pdb8G0R/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: 2.60 Å
• R-Value Free: 
  0.256 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

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

Lovell, S., Liu, L., 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: 233.67 kDa 
• Atom Count: 14,964 
• Modeled Residue Count: 1,939 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YHF (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth C]	5'-O-[(S)-(cyclopentyloxy)(hydroxy)phosphoryl]adenosine C15 H22 N5 O7 P ILDPDEYZUPQLBS-SDBHATRESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.256 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38G0R

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.922	α = 66.31
b = 86.971	β = 73.22
c = 105.19	γ = 89.12

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