4P3R

Cryogenic WT DHFR, time-averaged ensemble

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.109 
  • R-Value Observed: 0.111 

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This is version 1.5 of the entry. See complete history. 


Literature

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: 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 ...

    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. Electronic address: james.fraser@ucsf.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydrofolate reductaseA159Escherichia coli str. K-12 substr. DH10BMutation(s): 0 
Gene Names: folA, ECDH10B_0049
EC: 1.5.1.3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP
Download Ideal Coordinates CCD File 
C [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N		 Ligand Interaction
FOL
Query on FOL
Download Ideal Coordinates CCD File 
B [auth A]FOLIC ACID
C19 H19 N7 O6
OVBPIULPVIDEAO-LBPRGKRZSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.109 
  • R-Value Observed: 0.111 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.04α = 90
b = 44.82β = 90
c = 98.2γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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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: Structure summary
  • Version 1.3: 2016-07-27
    Changes: Data collection
  • Version 1.4: 2016-08-10
    Changes: Data collection
  • Version 1.5: 2017-11-22
    Changes: Derived calculations, Refinement description, Structure summary