Ensemble model for Escherichia coli dihydrofolate reductase at 277K

Experimental Data Snapshot

  • Resolution: 1.05 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 

wwPDB Validation 

Currently 4PTJ does not have a validation slider image.

This is version 1.3 of the entry. See complete history


Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR.

Keedy, D.A.van den Bedem, H.Sivak, D.A.Petsko, G.A.Ringe, D.Wilson, M.A.Fraser, J.S.

(2014) Structure 22: 899-910

  • DOI: https://doi.org/10.1016/j.str.2014.04.016
  • Primary Citation of Related Structures:  
    4P3Q, 4P3R, 4PSS, 4PST, 4PTH, 4PTJ

  • PubMed Abstract: 

    Most macromolecular X-ray structures are determined from cryocooled crystals, but it is unclear whether cryocooling distorts functionally relevant flexibility. Here we compare independently acquired pairs of high-resolution data sets of a model Michaelis complex of dihydrofolate reductase (DHFR), collected by separate groups at both room and cryogenic temperatures. These data sets allow us to isolate the differences between experimental procedures and between temperatures. Our analyses of multiconformer models and time-averaged ensembles suggest that cryocooling suppresses and otherwise modifies side-chain and main-chain conformational heterogeneity, quenching dynamic contact networks. Despite some idiosyncratic differences, most changes from room temperature to cryogenic temperature are conserved and likely reflect temperature-dependent solvent remodeling. Both cryogenic data sets point to additional conformations not evident in the corresponding room temperature data sets, suggesting that cryocooling does not merely trap preexisting conformational heterogeneity. Our results demonstrate that crystal cryocooling consistently distorts the energy landscape of DHFR, a paragon for understanding functional protein dynamics.

  • Organizational Affiliation

    Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrofolate reductase159Escherichia coli str. K-12 substr. DH10BMutation(s): 0 
Gene Names: folAECDH10B_0049
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CSD
Experimental Data & Validation

Experimental Data

  • Resolution: 1.05 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.299α = 90
b = 45.521β = 90
c = 98.711γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SHELXmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

Currently 4PTJ does not have a validation slider image.

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-06-25
    Changes: Database references
  • Version 1.2: 2014-11-12
    Changes: Non-polymer description, Structure summary
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description