Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.65 kDa 
• Atom Count: 1385 
• Modelled Residue Count: 164 
• Deposited Residue Count: 164 
• Unique protein chains: 1

3QYU

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

• DOI: 10.2210/pdb3QYU/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-03-04 Released: 2011-08-24 
• Deposition Author(s): Colliandre, L., Gelin, M., Labesse, G., Guichou, J.-F.

---

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 

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

• PubMed: 21904027 
• 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase F	A	164	Homo sapiens	Mutation(s): 1  Gene Names: PPIF, CYP3 EC: 5.2.1.8
Find proteins for P30405 (Homo sapiens) Explore P30405  Go to UniProtKB:  P30405
NIH Common Fund Data Resources
PHAROS:  P30405 GTEx:  ENSG00000108179

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 = 57.927	α = 90
b = 57.927	β = 90
c = 88.537	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-03-04 
• Released Date: 2011-08-24 
Deposition Author(s): Colliandre, L., Gelin, M., Labesse, G., Guichou, J.-F.

Revision History  

• 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