3LRP | pdb_00003lrp

Crystal Structure of Plasmodium falciparum ADP-Ribosylation Factor 1

• PDB DOI: https://doi.org/10.2210/pdb3LRP/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-11 Released: 2010-11-10 
• Deposition Author(s): Cook, W.J., Chattopadhyay, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Structure of Plasmodium falciparum ADP-ribosylation factor 1.

Cook, W.J., Smith, C.D., Senkovich, O., Holder, A.A., Chattopadhyay, D.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1426-1431

• PubMed: 21045287 
• DOI: https://doi.org/10.1107/S1744309110036997
• Primary Citation of Related Structures:  
  3LRP


• PubMed Abstract: 
  

  Vesicular trafficking may play a crucial role in the pathogenesis and survival of the malaria parasite. ADP-ribosylation factors (ARFs) are among the major components of vesicular trafficking pathways in eukaryotes. The crystal structure of ARF1 GTPase from Plasmodium falciparum has been determined in the GDP-bound conformation at 2.5 Å resolution and is compared with the structures of mammalian ARF1s.

---

Organizational Affiliation: 

University of Alabama at Birmingham, Birmingham, AL 35294, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21.5 kDa 
• Atom Count: 1,600 
• Modelled Residue Count: 181 
• Deposited Residue Count: 181 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor 1	A	181	Plasmodium falciparum	Mutation(s): 0  Gene Names: ARF1, ARF, PLARF EC: 3.6.5.2
UniProt
Find proteins for Q7KQL3 (Plasmodium falciparum (isolate 3D7)) Explore Q7KQL3  Go to UniProtKB:  Q7KQL3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.732	α = 90
b = 147.28	β = 90
c = 64.229	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-10 
Deposition Author(s): Cook, W.J., Chattopadhyay, D.

Revision History  

• Version 1.0: 2010-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-06-19
  Changes: Database references
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description