6WHP | pdb_00006whp

Structure of Choline kinase from Cryptococcus neoformans var. grubii serotype A

• PDB DOI: https://doi.org/10.2210/pdb6WHP/pdb

• Classification: TRANSFERASE
• Organism(s): Cryptococcus neoformans H99
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-04-08 Released: 2020-04-22 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Models: experimental

Literature

Structure of Choline kinase from Cryptococcus neoformans var. grubii serotype A

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.45 kDa 
• Atom Count: 3,508 
• Modeled Residue Count: 428 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choline kinase	A	440	Cryptococcus neoformans H99	Mutation(s): 0  Gene Names: CNAG_04408
UniProt
Find proteins for J9VWY8 (Cryptococcus neoformans (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)) Explore J9VWY8  Go to UniProtKB:  J9VWY8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36whp

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.5	α = 90
b = 129.5	β = 90
c = 160.01	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-22 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2020-04-22
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references
• Version 1.2: 2024-04-03
  Changes: Refinement description