3O4Y | pdb_00003o4y

Crystal structure of CAD domain of the Plasmodium Vivax CDPK, PVX_11610

• PDB DOI: https://doi.org/10.2210/pdb3O4Y/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium vivax
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-27 Released: 2010-08-25 
• Deposition Author(s): Wernimont, A.K., Hutchinson, A., Sullivan, H., Weadge, J., Bochkarev, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Hui, R., Amani, M., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.275 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.279 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of CAD domain of the Plasmodium Vivax CDPK, PVX_11610

Wernimont, A.K., Hutchinson, A., Sullivan, H., Weadge, J., Bochkarev, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Hui, R., Amani, M.

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)

Macromolecule Content 

• Total Structure Weight: 22.92 kDa 
• Atom Count: 1,548 
• Modeled Residue Count: 172 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-dependent protein kinase 3	A	196	Plasmodium vivax	Mutation(s): 0  Gene Names: PVX_119610 EC: 2.7.11.1
UniProt
Find proteins for A5KBB4 (Plasmodium vivax (strain Salvador I)) Explore A5KBB4  Go to UniProtKB:  A5KBB4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.275 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.279 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.106	α = 90
b = 84.858	β = 90
c = 85.757	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-25 
Deposition Author(s): Wernimont, A.K., Hutchinson, A., Sullivan, H., Weadge, J., Bochkarev, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Hui, R., Amani, M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description