4JWQ | pdb_00004jwq

Crystal Structure of the Calcium Binding Domain of CDPK3 from Plasmodium Berghei, PB000947.00

• PDB DOI: https://doi.org/10.2210/pdb4JWQ/pdb

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


• Deposited: 2013-03-27 Released: 2013-04-17 
• Deposition Author(s): Wernimont, A.K., Loppnau, P., Lin, Y.H., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Hui, R., Mottaghi, K., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.236 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Crystal Structure of the Calcium Binding Domain of CDPK3 from Plasmodium Berghei, PB000947.00

Wernimont, A.K., Loppnau, P., Lin, Y.H., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Hui, R., Mottaghi, K.

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: 46.33 kDa 
• Atom Count: 1,195 
• Modeled Residue Count: 142 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-dependent protein kinase	A, B [auth C]	199	Plasmodium berghei ANKA	Mutation(s): 0  Gene Names: PB000947.00.0, PBANKA_040820

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	C [auth A], D [auth A], E [auth C], F [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.236 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.564	α = 90
b = 69.741	β = 90
c = 90.581	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-17 
Deposition Author(s): Wernimont, A.K., Loppnau, P., Lin, Y.H., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Hui, R., Mottaghi, K., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2013-04-17
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Refinement description