4RGJ | pdb_00004rgj

Apo crystal structure of CDPK4 from Plasmodium falciparum, PF3D7_0717500

• PDB DOI: https://doi.org/10.2210/pdb4RGJ/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium falciparum
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-09-30 Released: 2014-10-29 
• Deposition Author(s): Wernimont, A.K., Walker, J.R., Hutchinson, A., Seitova, A., He, H., Loppnau, P., Neculai, M., Amani, M., Lin, Y.H., Ravichandran, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Lovato, D.V., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.255 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Apo crystal structure of CDPK4 from Plasmodium falciparum, PF3D7_0717500

Wernimont, A.K., Walker, J.R., Hutchinson, A., Seitova, A., He, H., Loppnau, P., Neculai, M., Amani, M., Lin, Y.H., Ravichandran, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Lovato, D.V.

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: 60 kDa 
• Atom Count: 3,823 
• Modeled Residue Count: 463 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-dependent protein kinase 4	A	520	Plasmodium falciparum	Mutation(s): 0  Gene Names: CDPK4, CPK4, PF07_0072 EC: 2.7.11.1
UniProt
Find proteins for Q8IBS5 (Plasmodium falciparum (isolate 3D7)) Explore Q8IBS5  Go to UniProtKB:  Q8IBS5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.255 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.654	α = 90
b = 75.548	β = 90
c = 92.562	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: 2014-10-29 
Deposition Author(s): Wernimont, A.K., Walker, J.R., Hutchinson, A., Seitova, A., He, H., Loppnau, P., Neculai, M., Amani, M., Lin, Y.H., Ravichandran, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Lovato, D.V., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-10-29
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description