3Q5I | pdb_00003q5i

Crystal Structure of PBANKA_031420

• PDB DOI: https://doi.org/10.2210/pdb3Q5I/pdb

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


• Deposited: 2010-12-28 Released: 2011-06-01 
• Deposition Author(s): Wernimont, A.K., Hutchinson, A., Sullivan, H., Panico, E., Crombet, L., Cossar, D., Hassani, A., Vedadi, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Hui, R., Neculai, A.M., Amani, M., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.250 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of CDPK1 from Plasmodium Bergheii, PBANKA_031420

Wernimont, A.K., Hutchinson, A., Sullivan, H., Panico, E., Crombet, L., Cossar, D., Hassani, A., Vedadi, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Hui, R., Neculai, A.M., 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: 59.74 kDa 
• Atom Count: 4,011 
• Modeled Residue Count: 470 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein kinase	A	504	Plasmodium berghei	Mutation(s): 0  Gene Names: PB000158.03.0, PBANKA_031420 EC: 2.7.11.1
UniProt
Find proteins for A0A509AHB6 (Plasmodium berghei (strain Anka)) Explore A0A509AHB6  Go to UniProtKB:  A0A509AHB6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	H [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
CA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.250 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.467	α = 90
b = 107.138	β = 108.21
c = 54.303	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PHASER	phasing
TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-01 
Deposition Author(s): Wernimont, A.K., Hutchinson, A., Sullivan, H., Panico, E., Crombet, L., Cossar, D., Hassani, A., Vedadi, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Hui, R., Neculai, A.M., Amani, M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2011-06-01
  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: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description