1D3F | pdb_00001d3f

N-TERMINAL DOMAIN CORE METHIONINE MUTATION

• PDB DOI: https://doi.org/10.2210/pdb1D3F/pdb

• Classification: HYDROLASE
• Organism(s): Tequatrovirus T4
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-09-29 Released: 1999-10-08 
• Deposition Author(s): Gassner, N.C., Matthews, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Work: 
  0.159 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

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

• PubMed: 10666571 
• DOI: https://doi.org/10.1107/s0907444999013347
• Primary Citation Related Structures: 
  1CX7, 1D2W, 1D2Y, 1D3F, 1D3J, 1D3M, 1D3N


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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.87 kDa 
• Atom Count: 1,418 
• Modeled Residue Count: 162 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME	A	164	Tequatrovirus T4	Mutation(s): 3  Gene Names: GENE E EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HED	D [auth A]	2-HYDROXYETHYL DISULFIDE C4 H10 O2 S2 KYNFOMQIXZUKRK-UHFFFAOYSA-N
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Work:  0.159 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.97	α = 90
b = 60.97	β = 90
c = 97.07	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-10-08 
Deposition Author(s): Gassner, N.C., Matthews, B.W.

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
• Version 1.4: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.5: 2024-02-07
  Changes: Data collection