3QYU

Crystal structure of human cyclophilin D at 1.54 A resolution at room temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

In-plate protein crystallization, in situ ligand soaking and X-ray diffraction.

le Maire, A.Gelin, M.Pochet, S.Hoh, F.Pirocchi, M.Guichou, J.F.Ferrer, J.L.Labesse, G.

(2011) Acta Crystallogr D Biol Crystallogr 67: 747-755

  • DOI: 10.1107/S0907444911023249
  • Primary Citation of Related Structures:  
    3QYU, 3QYW, 3QYZ

  • PubMed Abstract: 
  • X-ray crystallography is now a recognized technique for ligand screening, especially for fragment-based drug design. However, protein crystal handling is still tedious and limits further automation. An alternative method for the solution of crystal structures of proteins in complex with small ligands is proposed ...

    X-ray crystallography is now a recognized technique for ligand screening, especially for fragment-based drug design. However, protein crystal handling is still tedious and limits further automation. An alternative method for the solution of crystal structures of proteins in complex with small ligands is proposed. Crystallization drops are directly exposed to an X-ray beam after cocrystallization or soaking with the desired ligands. The use of dedicated plates in connection with an optimal parametrization of the G-rob robot allows efficient data collection. Three proteins currently under study in our laboratory for ligand screening by X-ray crystallography were used as validation test cases. The protein crystals belonged to different space groups, including a challenging monoclinic case. The resulting diffraction data can lead to clear ligand recognition, including indication of alternating conformations. These results demonstrate a possible method for automation of ligand screening by X-ray crystallography.


    Organizational Affiliation

    Université Montpellier 1 et 2, Centre de Biochimie Structurale, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase F A164Homo sapiensMutation(s): 1 
Gene Names: PPIFCYP3
EC: 5.2.1.8
Find proteins for P30405 (Homo sapiens)
Explore P30405 
Go to UniProtKB:  P30405
NIH Common Fund Data Resources
PHAROS:  P30405
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.927α = 90
b = 57.927β = 90
c = 88.537γ = 90
Software Package:
Software NamePurpose
DNAdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2012-03-21
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description