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: 18841.47 
• Atom Count: 1317 
• Residue Count: 164 
• Unique protein chains: 1

1G06

CRYSTAL STRUCTURE OF T4 LYSOZYME MUTANT V149S

• DOI: 10.2210/pdb1G06/pdb

• Classification: HYDROLASE
• Organism(s): Enterobacteria phage T4
• Expression System: Escherichia coli
• Mutation(s): 3 


• Deposited: 2000-10-05 Released: 2001-05-23 
• Deposition Author(s): Xu, J., Baase, W.A., Quillin, M.L., Matthews, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Work: 0.156 

Literature

Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme.

Xu, J., Baase, W.A., Quillin, M.L., Baldwin, E.P., Matthews, B.W.

(2001) Protein Sci. 10: 1067-1078

• PubMed: 11316887 
• DOI: 10.1110/ps.02101
• Primary Citation of Related Structures:  
  1G0Q, 1G0P, 1G0M, 1G0L, 1G0K, 1G0J, 1G0G, 1G07, 1I6S, 1G1W, 1G1V


• PubMed Abstract: 
  

To investigate the structural and thermodynamic basis of the binding of solvent at internal sites within proteins a number of mutations were constructed in T4 lysozyme. Some of these were designed to introduce new solvent-binding sites. Others were intended to displace solvent from preexisting sites. In one case Val-149 was replaced with alanine, serine, cysteine, threonine, isoleucine, and glycine. Crystallographic analysis shows that, with the exception of isoleucine, each of these substitutions results in the binding of solvent at a polar site that is sterically blocked in the wild-type enzyme. Mutations designed to perturb or displace a solvent molecule present in the native enzyme included the replacement of Thr-152 with alanine, serine, cysteine, valine, and isoleucine. Although the solvent molecule was moved in some cases by up to 1.7 A, in no case was it completely removed from the folded protein. The results suggest that hydrogen bonds from the protein to bound solvent are energy neutral. The binding of solvent to internal sites within proteins also appears to be energy neutral except insofar as the bound solvent may prevent a loss of energy due to potential hydrogen bonding groups that would otherwise be unsatisfied. The introduction of a solvent-binding site appears to require not only a cavity to accommodate the water molecule but also the presence of polar groups to help satisfy its hydrogen-bonding potential. It may be easier to design a site to accommodate two or more water molecules rather than one as the solvent molecules can then hydrogen-bond to each other. For similar reasons it is often difficult to design a point mutation that will displace a single solvent molecule from the core of a protein.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (LYSOZYME)	A	164	Enterobacteria phage T4	Mutation(s): 3  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: 1.85 Å
• R-Value Work: 0.156 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 60.840	α = 90.00
b = 60.840	β = 90.00
c = 96.820	γ = 120.00

Software Package:

Software Name	Purpose
UCSD-system	data scaling
SDMS	data reduction
TNT	refinement
TNT	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-10-05 
• Released Date: 2001-05-23 
• Deposition Author(s): Xu, J., Baase, W.A., Quillin, M.L., Matthews, B.W.

Revision History 

• Version 1.0: 2001-05-23
  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: 2017-10-04
  Type: Refinement description