6K77 | pdb_00006k77

Crystal structure of AMPPNP bound Ck1a alpha from C. neoformans

• PDB DOI: https://doi.org/10.2210/pdb6K77/pdb

• Classification: TRANSFERASE
• Organism(s): Cryptococcus neoformans Bt85
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-06-06 Released: 2020-06-10 
• Deposition Author(s): Cho, H.S., Yoo, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.282 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of AMPPNP bound Cka1 alpha from C. neoformans

Cho, H.S., Yoo, Y.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.4 kDa 
• Atom Count: 2,835 
• Modeled Residue Count: 330 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A	338	Cryptococcus neoformans Bt85	Mutation(s): 0  Gene Names: C365_06417

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
SO4	D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.282 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.283	α = 90
b = 95.853	β = 90
c = 93.396	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-10 
Deposition Author(s): Cho, H.S., Yoo, Y.

Revision History  

• Version 1.0: 2020-06-10
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description