3BFK | pdb_00003bfk

Crystal structure of Plasmodium falciparum Rab11a in complex with GDP

• PDB DOI: https://doi.org/10.2210/pdb3BFK/pdb

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


• Deposited: 2007-11-21 Released: 2007-12-04 
• Deposition Author(s): Pizarro, J.C., Sukumar, D., Hassanali, A., Lin, L., Wernimont, A.K., Lew, J., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Bochkarev, A., Hui, R., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.259 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Plasmodium falciparum Rab11a in complex with GDP.

Pizarro, J.C., Sukumar, D., Hassanali, A., Lin, L., Wernimont, A.K., Lew, J., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Bochkarev, A., Hui, R.

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)

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 105.93 kDa 
• Atom Count: 7,472 
• Modeled Residue Count: 825 
• Deposited Residue Count: 905 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Small GTPase Rab11	A, B, C, D, E	181	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PF13_0119 EC: 3.6.5.2
UniProt
Find proteins for Q76NM4 (Plasmodium falciparum (isolate 3D7)) Explore Q76NM4  Go to UniProtKB:  Q76NM4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	F [auth A], G [auth B], J [auth C], L [auth D], M [auth E]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
GOL	H [auth B], I [auth B], K [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.259 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.49	α = 90
b = 48.371	β = 92.36
c = 119.236	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-04 
Deposition Author(s): Pizarro, J.C., Sukumar, D., Hassanali, A., Lin, L., Wernimont, A.K., Lew, J., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Bochkarev, A., Hui, R., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-12-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description