2GZQ | pdb_00002gzq

Phosphatidylethanolamine-binding protein from Plasmodium vivax

• PDB DOI: https://doi.org/10.2210/pdb2GZQ/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Plasmodium vivax
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-05-11 Released: 2006-05-23 
• Deposition Author(s): Arakaki, T.L., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.180 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.165 (DCC) 

Starting Model: experimental

Literature

The structure of Plasmodium vivax phosphatidylethanolamine-binding protein suggests a functional motif containing a left-handed helix

Arakaki, T., Neely, H., Boni, E., Mueller, N., Buckner, F.S., Van Voorhis, W.C., Lauricella, A., DeTitta, G., Luft, J., Hol, W.G., Merritt, E.A.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 178-182

• PubMed: 17329808 
• DOI: https://doi.org/10.1107/S1744309107007580
• Primary Citation Related Structures: 
  2GZQ


• PubMed Abstract: 
  

  The structure of a putative Raf kinase inhibitor protein (RKIP) homolog from the eukaryotic parasite Plasmodium vivax has been studied to a resolution of 1.3 A using multiple-wavelength anomalous diffraction at the Se K edge. This protozoan protein is topologically similar to previously studied members of the phosphatidylethanolamine-binding protein (PEBP) sequence family, but exhibits a distinctive left-handed alpha-helical region at one side of the canonical phospholipid-binding site. Re-examination of previously determined PEBP structures suggests that the P. vivax protein and yeast carboxypeptidase Y inhibitor may represent a structurally distinct subfamily of the diverse PEBP-sequence family.

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Organizational Affiliation: 
• Structural Genomics of Pathogenic Protozoa Consortium, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.3 kDa 
• Atom Count: 1,932 
• Modeled Residue Count: 191 
• Deposited Residue Count: 200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylethanolamine-binding protein	A	200	Plasmodium vivax	Mutation(s): 0  Gene Names: hPf.PFL0955c
UniProt
Find proteins for A5K000 (Plasmodium vivax (strain Salvador I)) Explore A5K000  Go to UniProtKB:  A5K000

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.180 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.165 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.309	α = 90
b = 54.11	β = 90
c = 94.377	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-23 
Deposition Author(s): Arakaki, T.L., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

• Version 1.0: 2006-05-23
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary