1D2W

N-TERMINAL DOMAIN CORE METHIONINE MUTATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Use of differentially substituted selenomethionine proteins in X-ray structure determination.

Gassner, N.C.Matthews, B.W.

(1999) Acta Crystallogr D Biol Crystallogr 55: 1967-1970

  • DOI: 10.1107/s0907444999013347
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Using heavily methionine-substituted T4 lysozyme as an example, it is shown how the addition or deletion of a small number of methionines can simplify the location of selenium sites for use in MAD phasing. By comparing the X-ray data for a large numb ...

    Using heavily methionine-substituted T4 lysozyme as an example, it is shown how the addition or deletion of a small number of methionines can simplify the location of selenium sites for use in MAD phasing. By comparing the X-ray data for a large number of singly substituted lysozymes, it is shown that the optimal amino acid to be substituted by methionine is leucine, followed, in order of preference, by phenylalanine, isoleucine and valine. The identification of leucine as the first choice agrees with the ranking suggested by the Dayhoff mutation probability, i.e. by the frequency of amino-acid substitutions in the sequences of related proteins. The ranking of the second and subsequent choices, however, differ significantly.


    Related Citations: 
    • Methionine and Alanine Substitutions Show that the Formation of Wild-type-like Structure in the Carboxy-terminal Domain of T4 Lysozyme is a Rate-Limiting Step in Folding
      Gassner, N.C., Baase, W.A., Lindstrom, J.D., Lu, J., Dahlquist, F.W., Matthews, B.W.
      (1999) Biochemistry 38: 14451
    • A Test of the "jigsaw-puzzle" Model for Protein Folding by Multiple Methionine Substitutions within the Core of T4 lysozyme
      Gassner, N.C., Baase, W.A., Matthews, B.W.
      (1996) Proc Natl Acad Sci U S A 93: 12155
    • Structure of Bacteriophage T4 Lysozyme Refined at 1.7 A Resolution
      Weaver, L.H., Matthews, B.W.
      (1987) J Mol Biol 193: 189

    Organizational Affiliation

    Institute of Molecular Biology, Howard Hughes Medical Institute and Department of Physics, 1229 University of Oregon, Eugene, OR 97403-1229, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYMEA164Escherichia virus T4Mutation(s): 3 
Gene Names: GENE EE
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HED
Query on HED

Download CCD File 
A
2-HYDROXYETHYL DISULFIDE
C4 H10 O2 S2
KYNFOMQIXZUKRK-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.93α = 90
b = 60.93β = 90
c = 97.41γ = 120
Software Package:
Software NamePurpose
TNTrefinement
AUTOSTRATdata reduction
SDMSdata scaling
TNTphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation