3QL3

Re-refined coordinates for PDB entry 1RX2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


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: 1RX2


Literature

A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis.

Bhabha, G.Lee, J.Ekiert, D.C.Gam, J.Wilson, I.A.Dyson, H.J.Benkovic, S.J.Wright, P.E.

(2011) Science 332: 234-238

  • DOI: https://doi.org/10.1126/science.1198542
  • Primary Citation of Related Structures:  
    3QL0, 3QL3

  • PubMed Abstract: 

    Conformational dynamics play a key role in enzyme catalysis. Although protein motions have clear implications for ligand flux, a role for dynamics in the chemical step of enzyme catalysis has not been clearly established. We generated a mutant of Escherichia coli dihydrofolate reductase that abrogates millisecond-time-scale fluctuations in the enzyme active site without perturbing its structural and electrostatic preorganization. This dynamic knockout severely impairs hydride transfer. Thus, we have found a link between conformational fluctuations on the millisecond time scale and the chemical step of an enzymatic reaction, with broad implications for our understanding of enzyme mechanisms and for design of novel protein catalysts.


  • Organizational Affiliation

    Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrofolate reductase159Escherichia coli K-12Mutation(s): 0 
Gene Names: folAtmrAb0048JW0047
EC: 1.5.1.3
UniProt
Find proteins for P0ABQ4 (Escherichia coli (strain K12))
Explore P0ABQ4 
Go to UniProtKB:  P0ABQ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABQ4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.32α = 90
b = 45.51β = 90
c = 98.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-10
    Changes: Other
  • Version 1.3: 2011-09-28
    Changes: Other
  • Version 1.4: 2012-04-25
    Changes: Other
  • Version 1.5: 2014-11-12
    Changes: Structure summary
  • Version 1.6: 2024-02-21
    Changes: Data collection, Database references, Derived calculations