3CLV | pdb_00003clv

Crystal Structure of Rab5a from plasmodium falciparum, PFB0500c

• PDB DOI: https://doi.org/10.2210/pdb3CLV/pdb

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


• Deposited: 2008-03-20 Released: 2008-07-15 
• Deposition Author(s): Chattopadhyay, D., Wernimont, A.K., Langsley, G., Lew, J., Kozieradzki, I., Cossar, D., Schapira, M., Bochkarev, A., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Hui, R., Sukumar, D., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.252 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Crystal Structure of Rab5a from plasmodium falciparum, PFB0500c

Chattopadhyay, D., Wernimont, A.K., Langsley, G., Lew, J., Kozieradzki, I., Cossar, D., Schapira, M., Bochkarev, A., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Hui, R., Sukumar, D.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 24.18 kDa 
• Atom Count: 1,532 
• Modeled Residue Count: 175 
• Deposited Residue Count: 208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rab5 protein, putative	A	208	Plasmodium falciparum	Mutation(s): 0  Gene Names: PFB0500c EC: 3.6.5.2
UniProt
Find proteins for O96193 (Plasmodium falciparum (isolate 3D7)) Explore O96193  Go to UniProtKB:  O96193

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	D [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.252 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.964	α = 90
b = 66.964	β = 90
c = 76.128	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): Chattopadhyay, D., Wernimont, A.K., Langsley, G., Lew, J., Kozieradzki, I., Cossar, D., Schapira, M., Bochkarev, A., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Hui, R., Sukumar, D., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations