2BIT | pdb_00002bit

Crystal structure of human cyclophilin D at 1.7 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2BIT/pdb

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


• Deposited: 2005-01-26 Released: 2005-01-26 
• Deposition Author(s): Hennig, M., Thoma, R., Stihle, M., Schlatter, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.175 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Starting Model: experimental

Literature

Crystal Engineering Yields Crystals of Cyclophilin D Diffracting to 1.7 A Resolution

Schlatter, D., Thoma, R., Kueng, E., Stihle, M., Mueller, F., Boroni, E., Hennig, M.

(2005) Acta Crystallogr D Biol Crystallogr 61: 513-519

• PubMed: 15858260 
• DOI: https://doi.org/10.1107/S0907444905003070
• Primary Citation Related Structures: 
  2BIT, 2BIU


• PubMed Abstract: 
  

  In the pharmaceutical industry, knowledge of the three-dimensional structure of a specific target facilitates the drug-discovery process. Despite possessing favoured analytical properties such as high purity and monodispersion in light scattering, some proteins are not capable of forming crystals suitable for X-ray analysis. Cyclophilin D, an isoform of cyclophilin that is expressed in the mitochondria, was selected as a drug target for the treatment of cardiac disorders. As the wild-type enzyme defied all attempts at crystallization, protein engineering on the enzyme surface was performed. The K133I mutant gave crystals that diffracted to 1.7 A resolution using in-house X-ray facilities and were suitable for soaking experiments. The crystals were very robust and diffraction was maintained after soaking in 25% DMSO solution: excellent conditions for the rapid analysis of complex structures including crystallographic fragment screening.

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Organizational Affiliation: 
• F. Hoffmann-La Roche Ltd, Pharmaceutical Research Discovery, CH-4070 Basel, Switzerland. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 17.74 kDa 
• Atom Count: 1,633 
• Modeled Residue Count: 164 
• Deposited Residue Count: 165 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE	A [auth X]	165	Homo sapiens	Mutation(s): 1  EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P30405 (Homo sapiens) Explore P30405  Go to UniProtKB:  P30405
PHAROS:  P30405 GTEx:  ENSG00000108179

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.175 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.165	α = 90
b = 57.165	β = 90
c = 87.227	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-26 
Deposition Author(s): Hennig, M., Thoma, R., Stihle, M., Schlatter, D.

Revision History  

• Version 1.0: 2005-01-26
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-06-13
  Changes: Data collection, Database references
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description