6CKG

D-glycerate 3-kinase from Cryptococcus neoformans var. grubii serotype A (H99 / ATCC 208821 / CBS 10515 / FGSC 9487)

• PDB DOI: https://doi.org/10.2210/pdb6CKG/pdb

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


• Deposited: 2018-02-28 Released: 2018-04-04 
• Deposition Author(s): Horanyi, P.S., Abendroth, J., Lorimer, D.D., Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.225 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Literature

D-glycerate 3-kinase from Cryptococcus neoformans var. grubii serotype A (H99 / ATCC 208821 / CBS 10515 / FGSC 9487)

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

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 74.82 kDa 
• Atom Count: 5,232 
• Modelled Residue Count: 582 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-glycerate 3-kinase	A, B	330	Cryptococcus neoformans var. grubii H99	Mutation(s): 0  Gene Names: CNAG_07779 EC: 2.7.1.31
UniProt
Find proteins for J9VS00 (Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)) Explore J9VS00  Go to UniProtKB:  J9VS00

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.225 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M36CKG

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.74	α = 90
b = 87.76	β = 90
c = 103.11	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MoRDa	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-04 
Deposition Author(s): Horanyi, P.S., Abendroth, J., Lorimer, D.D., Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-04-04
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references