Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18586.20 
• Atom Count: 1299 
• Residue Count: 162 
• Unique protein chains: 1

2B6Z

T4 Lysozyme mutant L99A at ambient pressure

• DOI: 10.2210/pdb2B6Z/pdb

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


• Deposited: 2005-10-03 Released: 2005-11-08 
• Deposition Author(s): Collins, M.D., Quillin, M.L., Matthews, B.W., Gruner, S.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.197 
• R-Value Work: 0.144 

Literature

Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation

Collins, M.D., Hummer, G., Quillin, M.L., Matthews, B.W., Gruner, S.M.

(2005) Proc.Natl.Acad.Sci.Usa 102: 16668-16671

• PubMed: 16269539 
• DOI: 10.1073/pnas.0508224102
• Primary Citation of Related Structures:  
  2OE4, 2B75, 2B74, 2B73, 2B72, 2B70, 2B6Y, 2B6X, 2B6W
• Also Cited By: 2OEA, 2OE9, 2OE7


• PubMed Abstract: 
  

Formation of a water-expelling nonpolar core is the paradigm of protein folding and stability. Although experiment largely confirms this picture, water buried in "hydrophobic" cavities is required for the function of some proteins. Hydration of the protein core has also been suggested as the mechanism of pressure-induced unfolding. We therefore are led to ask whether even the most nonpolar protein core is truly hydrophobic (i.e., water-repelling). To answer this question we probed the hydration of an approximately 160-A(3), highly hydrophobic cavity created by mutation in T4 lysozyme by using high-pressure crystallography and molecular dynamics simulation. We show that application of modest pressure causes approximately four water molecules to enter the cavity while the protein itself remains essentially unchanged. The highly cooperative filling is primarily due to a small change in bulk water activity, which implies that changing solvent conditions or, equivalently, cavity polarity can dramatically affect interior hydration of proteins and thereby influence both protein activity and folding.

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Organizational Affiliation: 

Department of Physics, Cornell University, Ithaca, NY 14853, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysozyme	A	162	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
BME	A	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.197 
• R-Value Work: 0.144 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 60.954	α = 90.00
b = 60.954	β = 90.00
c = 96.607	γ = 120.00

Software Package:

Software Name	Purpose
Adxv	data processing
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-03 
• Released Date: 2005-11-08 
• Deposition Author(s): Collins, M.D., Quillin, M.L., Matthews, B.W., Gruner, S.M.

Revision History 

• Version 1.0: 2005-11-08
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-11
  Type: Refinement description