Crystal structure of wild type cytochrome c peroxidase

Experimental Data Snapshot

  • Resolution: 2.66 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history


One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites.

Fischer, M.Shoichet, B.K.Fraser, J.S.

(2015) Chembiochem 16: 1560-1564

  • DOI: https://doi.org/10.1002/cbic.201500196
  • Primary Citation of Related Structures:  
    4XV4, 4XV5, 4XV6, 4XV7, 4XV8, 4XVA

  • PubMed Abstract: 

    Interrogating fragment libraries by X-ray crystallography is a powerful strategy for discovering allosteric ligands for protein targets. Cryocooling of crystals should theoretically increase the fraction of occupied binding sites and decrease radiation damage. However, it might also perturb protein conformations that can be accessed at room temperature. Using data from crystals measured consecutively at room temperature and at cryogenic temperature, we found that transient binding sites could be abolished at the cryogenic temperatures employed by standard approaches. Changing the temperature at which the crystallographic data was collected could provide a deliberate perturbation to the equilibrium of protein conformations and help to visualize hidden sites with great potential to allosterically modulate protein function.

  • Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St., Byers Hall, BH-501, Box 2550, San Francisco, CA 94158 (USA).

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c peroxidase, mitochondrialA,
B [auth C],
C [auth E],
D [auth G]
293Saccharomyces cerevisiae S288CMutation(s): 0 
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00431 
Go to UniProtKB:  P00431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00431
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.66 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.11α = 90
b = 104.76β = 90
c = 185.25γ = 90
Software Package:
Software NamePurpose
xia2data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM59957
National Institutes of Health/Office of the DirectorUnited StatesOD009180
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM110580
National Science Foundation (NSF, United States)United StatesSTC-1231306

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-06-24
    Changes: Database references
  • Version 1.2: 2015-07-29
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Advisory, Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.5: 2024-02-28
    Changes: Data collection, Database references, Derived calculations