Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18943.71 
• Atom Count: 1302 
• Residue Count: 164 
• Unique protein chains: 1

1D3M

METHIONINE CORE MUTATION

• DOI: 10.2210/pdb1D3M/pdb

• Classification: HYDROLASE
• Organism(s): Enterobacteria phage T4
• Expression System: Escherichia coli
• Mutation(s): 7 


• Deposited: 1999-09-29 Released: 1999-09-30 
• Deposition Author(s): Gassner, N.C., Matthews, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Work: 0.158 

Literature

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

Gassner, N.C., Matthews, B.W.

(1999) Acta Crystallogr.,Sect.D 55: 1967-1970

• PubMed: 10666571 
• Primary Citation of Related Structures:  
  1D3N, 1D3J, 1D3F, 1D2Y, 1D2W, 1CX7


• 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 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.

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Related Citations: 

• 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.USA 93: 12155
• 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
• Structure of Bacteriophage T4 Lysozyme Refined at 1.7 A Resolution
  Weaver, L.H.,Matthews, B.W.
  (1987) J.Mol.Biol. 193: 189




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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
Molecule	Chains	Sequence Length	Organism	Details
LYSOZYME	A	164	Enterobacteria phage T4	Mutation(s): 7  Gene Names: E EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4) Go to UniProtKB:  P00720

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
HED	A	2-HYDROXYETHYL DISULFIDE C4 H10 O2 S2 KYNFOMQIXZUKRK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Work: 0.158 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 61.180	α = 90.00
b = 61.180	β = 90.00
c = 96.560	γ = 120.00

Software Package:

Software Name	Purpose
AUTOSTRAT	data reduction
SDMS	data scaling
TNT	phasing
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-09-29 
• Released Date: 1999-09-30 
• Deposition Author(s): Gassner, N.C., Matthews, B.W.

Revision History 

• Version 1.0: 1999-09-30
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-01-31
  Type: Experimental preparation