2AMX

Crystal structure of Plasmodium Yoelii Adenosine deaminase (PY02076)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.

Vedadi, M.Lew, J.Artz, J.Amani, M.Zhao, Y.Dong, A.Wasney, G.A.Gao, M.Hills, T.Brokx, S.Qiu, W.Sharma, S.Diassiti, A.Alam, Z.Melone, M.Mulichak, A.Wernimont, A.Bray, J.Loppnau, P.Plotnikova, O.Newberry, K.Sundararajan, E.Houston, S.Walker, J.Tempel, W.Bochkarev, A.Kozieradzki, I.Edwards, A.Arrowsmith, C.Roos, D.Kain, K.Hui, R.

(2007) Mol.Biochem.Parasitol. 151: 100-110

  • DOI: 10.1016/j.molbiopara.2006.10.011
  • Primary Citation of Related Structures:  1TXJ, 1Y6Z, 1YO3, 1Z6G, 1Z7D, 1Z81, 1ZO2, 2A22, 2A4A, 2AIF, 2AQW, 2AV4, 2AWP, 2AYV, 2B71, 2BDD, 2F4Z, 2FDS, 2FFC, 2FO3, 2FU0, 2FWK, 2GHI, 2H1R, 2H2Y, 2H66, 2HER, 2HJR, 2HTE, 2HVG, 3PGG, 3TB2, 1XCC
  • Also Cited By: 2F6I, 2Q58, 4L0U, 4L0W

  • PubMed Abstract: 
  • Parasites from the protozoan phylum Apicomplexa are responsible for diseases, such as malaria, toxoplasmosis and cryptosporidiosis, all of which have significantly higher rates of mortality and morbidity in economically underdeveloped regions of the ...

    Parasites from the protozoan phylum Apicomplexa are responsible for diseases, such as malaria, toxoplasmosis and cryptosporidiosis, all of which have significantly higher rates of mortality and morbidity in economically underdeveloped regions of the world. Advances in vaccine development and drug discovery are urgently needed to control these diseases and can be facilitated by production of purified recombinant proteins from Apicomplexan genomes and determination of their 3D structures. To date, both heterologous expression and crystallization of Apicomplexan proteins have seen only limited success. In an effort to explore the effectiveness of producing and crystallizing proteins on a genome-scale using a standardized methodology, over 400 distinct Plasmodium falciparum target genes were chosen representing different cellular classes, along with select orthologues from four other Plasmodium species as well as Cryptosporidium parvum and Toxoplasma gondii. From a total of 1008 genes from the seven genomes, 304 (30.2%) produced purified soluble proteins and 97 (9.6%) crystallized, culminating in 36 crystal structures. These results demonstrate that, contrary to previous findings, a standardized platform using Escherichia coli can be effective for genome-scale production and crystallography of Apicomplexan proteins. Predictably, orthologous proteins from different Apicomplexan genomes behaved differently in expression, purification and crystallization, although the overall success rates of Plasmodium orthologues do not differ significantly. Their differences were effectively exploited to elevate the overall productivity to levels comparable to the most successful ongoing structural genomics projects: 229 of the 468 target genes produced purified soluble protein from one or more organisms, with 80 and 32 of the purified targets, respectively, leading to crystals and ultimately structures from one or more orthologues.


    Organizational Affiliation

    Structural Genomics Consortium, U. of Toronto, 100 College St. Rm 522B, Toronto, Ont., Canada M5G 1L5.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
adenosine deaminase
A, B
376Plasmodium yoelii yoeliiN/A
Find proteins for Q7RMV2 (Plasmodium yoelii yoelii)
Go to UniProtKB:  Q7RMV2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download SDF File 
Download CCD File 
A, B
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A, B
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.719α = 90.00
b = 90.332β = 90.00
c = 137.086γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata reduction
ARP/wARPmodel building
REFMACrefinement
HKL-2000data scaling
RESOLVEphasing
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2005-09-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance