5KUV

Human cyclophilin A at 100K, Data set 8

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Conformational variation of proteins at room temperature is not dominated by radiation damage.

Russi, S., Gonzalez, A., Kenner, L.R., Keedy, D.A., Fraser, J.S., van den Bedem, H.

(2017) J Synchrotron Radiat 24: 73-82

  • DOI: 10.1107/S1600577516017343
  • Primary Citation of Related Structures:  
    5KXT, 5KXW, 5KXY, 5KXX, 5KXK, 5KXM, 5KXL, 5KXO, 5KXN, 5KXP

  • PubMed Abstract: 

    • Protein crystallography data collection at synchrotrons is routinely carried out at cryogenic temperatures to mitigate radiation damage. Although damage still takes place at 100 K and below, the immobilization of free radicals increases the lifetime of the crystals by approximately 100-fold ...

    Protein crystallography data collection at synchrotrons is routinely carried out at cryogenic temperatures to mitigate radiation damage. Although damage still takes place at 100 K and below, the immobilization of free radicals increases the lifetime of the crystals by approximately 100-fold. Recent studies have shown that flash-cooling decreases the heterogeneity of the conformational ensemble and can hide important functional mechanisms from observation. These discoveries have motivated increasing numbers of experiments to be carried out at room temperature. However, the trade-offs between increased risk of radiation damage and increased observation of alternative conformations at room temperature relative to cryogenic temperature have not been examined. A considerable amount of effort has previously been spent studying radiation damage at cryo-temperatures, but the relevance of these studies to room temperature diffraction is not well understood. Here, the effects of radiation damage on the conformational landscapes of three different proteins (T. danielli thaumatin, hen egg-white lysozyme and human cyclophilin A) at room (278 K) and cryogenic (100 K) temperatures are investigated. Increasingly damaged datasets were collected at each temperature, up to a maximum dose of the order of 10 7  Gy at 100 K and 10 5  Gy at 278 K. Although it was not possible to discern a clear trend between damage and multiple conformations at either temperature, it was observed that disorder, monitored by B-factor-dependent crystallographic order parameters, increased with higher absorbed dose for the three proteins at 100 K. At 278 K, however, the total increase in this disorder was only statistically significant for thaumatin. A correlation between specific radiation damage affecting side chains and the amount of disorder was not observed. This analysis suggests that elevated conformational heterogeneity in crystal structures at room temperature is observed despite radiation damage, and not as a result thereof.

    Organizational Affiliation: 

    Bioscience Department, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase A A164Homo sapiensMutation(s): 0 
Gene Names: PPIA, CYPA
EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens)
Explore P62937 
Go to UniProtKB:  P62937
NIH Common Fund Data Resources
PHAROS:  P62937
GTEx:  ENSG00000196262
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.316α = 90
b = 52.638β = 90
c = 89.263γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103393
Department of Energy (DOE, United States)United StatesDE-AC02-76SF00515
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: 2016-08-10
    Type: Initial release
  • Version 1.1: 2017-01-04
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence