5F66

High-resolution isotropic multiconformer synchrotron model of CypA at 273 K

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

  • Deposited: 2015-12-05 Released: 2015-12-30 
  • Deposition Author(s): Fraser, J.S.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; National Science Foundation (United States) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 4YUO - determined by Keedy, D.A., Kenner, L.R., Warkentin, M., Woldeyes, R.A., Thompson, M.C., Brewster, A.S., Van Benschoten, A.H., Baxter, E.L., Hopkins, J.B., Uervirojnangkoorn, M., McPhillips, S.E., Song, J., Mori, R.A., Holton, J.M., Weis, W.I., Brunger, A.T., Soltis, M., Lemke, H., Gonzalez, A., Sauter, N.K., Cohen, A.E., van den Bedem, H., Thorne, R.E., Fraser, J.S.  

Literature

Measuring and modeling diffuse scattering in protein X-ray crystallography.

Van Benschoten, A.H.Liu, L.Gonzalez, A.Brewster, A.S.Sauter, N.K.Fraser, J.S.Wall, M.E.

(2016) Proc.Natl.Acad.Sci.USA 113: 4069-4074

  • DOI: 10.1073/pnas.1524048113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, wh ...

    X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation-libration-screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering.


    Organizational Affiliation

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase A
A
165Homo sapiensMutation(s): 0 
Gene Names: PPIA (CYPA)
EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens)
Go to Gene View: PPIA
Go to UniProtKB:  P62937
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.910α = 90.00
b = 52.440β = 90.00
c = 89.120γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-12-05 
  • Released Date: 2015-12-30 
  • Deposition Author(s): Fraser, J.S.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM110580
National Science Foundation (United States)United StatesSTC-1231306

Revision History 

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references
  • Version 1.2: 2016-04-13
    Type: Database references
  • Version 1.3: 2016-06-15
    Type: Database references
  • Version 1.4: 2017-08-09
    Type: Database references, Derived calculations
  • Version 1.5: 2017-09-27
    Type: Author supporting evidence
  • Version 1.6: 2018-08-15
    Type: Data collection, Database references