2HAQ | pdb_00002haq

Crystal Structure of Cyclophilin A from Leishmania Donovani

• PDB DOI: https://doi.org/10.2210/pdb2HAQ/pdb

• Classification: ISOMERASE
• Organism(s): Leishmania donovani
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-06-13 Released: 2006-06-20 
• Deposition Author(s): Venugopal, V., Sen, B., Datta, A.K., Banerjee, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Structure of cyclophilin from Leishmania donovani at 1.97 A resolution.

Venugopal, V., Sen, B., Datta, A.K., Banerjee, R.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 60-64

• PubMed: 17277440 
• DOI: https://doi.org/10.1107/S1744309106056351
• Primary Citation Related Structures: 
  2HAQ


• PubMed Abstract: 
  

  The crystal structure of cyclophilin from Leishmania donovani (LdCyp) has been determined and refined at 1.97 A resolution to a crystallographic R factor of 0.178 (R(free) = 0.197). The structure was solved by molecular replacement using cyclophilin from Trypanosoma cruzi as the search model. LdCyp exhibits complete structural conservation of the cyclosporin-binding site with respect to the homologous human protein, as anticipated from LdCyp-cyclosporin binding studies. Comparisons with other cyclophilins show deviations primarily in the loop regions. The solvent structure encompassing the molecule has also been analyzed in some detail.

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Organizational Affiliation: 
• Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Sector 1, Block AF, Bidhan Nagar, Kolkata 700 064, India.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 19.09 kDa 
• Atom Count: 1,376 
• Modeled Residue Count: 166 
• Deposited Residue Count: 172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclophilin	A	172	Leishmania donovani	Mutation(s): 0  Gene Names: CYP EC: 5.2.1.8
UniProt
Find proteins for Q9U9R3 (Leishmania donovani) Explore Q9U9R3  Go to UniProtKB:  Q9U9R3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.59	α = 90
b = 48.59	β = 90
c = 141.19	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-20 
Deposition Author(s): Venugopal, V., Sen, B., Datta, A.K., Banerjee, R.

Revision History  

• Version 1.0: 2006-06-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Refinement description