3SUB | pdb_00003sub

Crystal structure of the catalytic domain of Plasmodium falciparum ARF GTPase activating protein

• PDB DOI: https://doi.org/10.2210/pdb3SUB/pdb

• Classification: HYDROLASE ACTIVATOR
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-11 Released: 2011-11-09 
• Deposition Author(s): Cook, W.J., Chattopadhyay, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Structure of the catalytic domain of Plasmodium falciparum ARF GTPase-activating protein (ARFGAP).

Cook, W.J., Senkovich, O., Chattopadhyay, D.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1339-1344

• PubMed: 22102228 
• DOI: https://doi.org/10.1107/S1744309111032507
• Primary Citation Related Structures: 
  3SUB


• PubMed Abstract: 
  

  The crystal structure of the catalytic domain of the ADP ribosylation factor GTPase-activating protein (ARFGAP) from Plasmodium falciparum has been determined and refined to 2.4 Å resolution. Multiwavength anomalous diffraction (MAD) data were collected utilizing the Zn(2+) ion bound at the zinc-finger domain and were used to solve the structure. The overall structure of the domain is similar to those of mammalian ARFGAPs. However, several amino-acid residues in the area where GAP interacts with ARF1 differ in P. falciparum ARFGAP. Moreover, a number of residues that form the dimer interface in the crystal structure are unique in P. falciparum ARFGAP.

---

Organizational Affiliation: 
• Department of Medicine, University of Alabama at Birmingham, CBSE-250, 1015 18th Street South, Birmingham, AL 35294, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.56 kDa 
• Atom Count: 2,299 
• Modeled Residue Count: 270 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor GTPase-activating protein	A, B	163	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PFL2140c
UniProt
Find proteins for Q8I4Y5 (Plasmodium falciparum (isolate 3D7)) Explore Q8I4Y5  Go to UniProtKB:  Q8I4Y5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.9	α = 90
b = 95.9	β = 90
c = 92.8	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-09 
Deposition Author(s): Cook, W.J., Chattopadhyay, D.

Revision History  

• Version 1.0: 2011-11-09
  Type: Initial release
  
• Version 1.1: 2012-03-28
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations