3HKO | pdb_00003hko

Crystal structure of a cdpk kinase domain from cryptosporidium Parvum, cgd7_40

• PDB DOI: https://doi.org/10.2210/pdb3HKO/pdb

• Classification: TRANSFERASE
• Organism(s): Cryptosporidium parvum Iowa II
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-25 Released: 2009-06-02 
• Deposition Author(s): Wernimont, A.K., Hutchinson, A., Wasney, G., Vedadi, M., MacKenzie, F., Kozieradzki, I., Cossar, D., Weigelt, J., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Botchkarev, A., Hui, R., Artz, J.D., Amani, M., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.246 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a cdpk kinase domain from cryptosporidium Parvum, cgd7_40

Wernimont, A.K., Hutchinson, A., Wasney, G., Vedadi, M., MacKenzie, F., Kozieradzki, I., Cossar, D., Weigelt, J., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Botchkarev, A., Hui, R., Amani, M.

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)

Macromolecule Content 

• Total Structure Weight: 40.29 kDa 
• Atom Count: 2,789 
• Modeled Residue Count: 319 
• Deposited Residue Count: 345 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands	A	345	Cryptosporidium parvum Iowa II	Mutation(s): 0  Gene Names: cgd7_40 EC: 2.7.11.1
UniProt
Find proteins for Q5CZ29 (Cryptosporidium parvum (strain Iowa II)) Explore Q5CZ29  Go to UniProtKB:  Q5CZ29

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	D [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.246 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.48	α = 90
b = 63.045	β = 90
c = 84.041	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MacCHESS	data collection
PHASER	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-02 
Deposition Author(s): Wernimont, A.K., Hutchinson, A., Wasney, G., Vedadi, M., MacKenzie, F., Kozieradzki, I., Cossar, D., Weigelt, J., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Botchkarev, A., Hui, R., Artz, J.D., Amani, M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.3: 2023-09-06
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description