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 

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.,Sect.D 67: 747-755

  • DOI: 10.1107/S0907444911023249
  • Primary Citation of Related Structures:  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 s ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase F
A
164Homo sapiensGene Names: PPIF (CYP3)
EC: 5.2.1.8
Find proteins for P30405 (Homo sapiens)
Go to Gene View: PPIF
Go to UniProtKB:  P30405
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.148 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.927α = 90.00
b = 57.927β = 90.00
c = 88.537γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling
DNAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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