4P3Q

Room-temperature WT DHFR, time-averaged ensemble


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.351 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.118 

wwPDB Validation 3D Report Full Report


This is version 1.4 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:  

  • 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 Micha ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductase
A
159N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

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Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FOL
Query on FOL

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Download CCD File 
A
FOLIC ACID
C19 H19 N7 O6
OVBPIULPVIDEAO-LBPRGKRZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.351 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.118 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.320α = 90.00
b = 45.510β = 90.00
c = 98.910γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-06-25
    Type: Database references
  • Version 1.2: 2014-11-12
    Type: Structure summary
  • Version 1.3: 2016-08-10
    Type: Data collection
  • Version 1.4: 2017-11-22
    Type: Derived calculations, Refinement description, Structure summary