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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19126.51 
• Atom Count: 1323 
• Residue Count: 164 
• Unique protein chains: 1

3G3W

Crystal structure of spin labeled T4 Lysozyme (T151R1) at 291 K

• DOI: 10.2210/pdb3G3W/pdb

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


• Deposited: 2009-02-02 Released: 2009-05-05 
• Deposition Author(s): Fleissner, M.R., Cascio, D., Hubbell, W.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.216 
• R-Value Work: 0.171 

Literature

Structural origin of weakly ordered nitroxide motion in spin-labeled proteins.

Fleissner, M.R., Cascio, D., Hubbell, W.L.

(2009) Protein Sci. 18: 893-908

• PubMed: 19384990 
• DOI: 10.1002/pro.96
• Primary Citation of Related Structures:  
  3G3X, 3G3V, 2CUU, 1ZYT


• PubMed Abstract: 
  

A disulfide-linked nitroxide side chain (R1) used in site-directed spin labeling of proteins often exhibits an EPR spectrum characteristic of a weakly ordered z-axis anisotropic motion at topographically diverse surface sites, including those on helices, loops and edge strands of beta-sheets. To elucidate the origin of this motion, the first crystal structures of R1 that display simple z-axis anisotropic motion at solvent-exposed helical sites (131 and 151) and a loop site (82) in T4 lysozyme have been determined. Structures of 131R1 and 151R1 determined at cryogenic or ambient temperature reveal an intraresidue C(alpha)--H...S(delta) interaction that immobilizes the disulfide group, consistent with a model in which the internal motions of R1 are dominated by rotations about the two terminal bonds (Columbus, Kálai, Jeko, Hideg, and Hubbell, Biochemistry 2001;40:3828-3846). Remarkably, the 131R1 side chain populates two rotamers equally, but the EPR spectrum reflects a single dominant dynamic population, showing that the two rotamers have similar internal motion determined by the common disulfide-backbone interaction. The anisotropic motion for loop residue 82R1 is also accounted for by a common disulfide-backbone interaction, showing that the interaction does not require a specific secondary structure. If the above observations prove to be general, then significant variations in order and rate for R1 at noninteracting solvent-exposed helical and loop sites can be assigned to backbone motion because the internal motion is essentially constant.

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Organizational Affiliation: 

Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-7008.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysozyme	A	164	Enterobacteria phage T4	Mutations: A97C, C151T, T54C Gene Names: E EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4) Go to UniProtKB:  P00720

Small Molecules

Ligands 4 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
AZI	A	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N
MTN	A	S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate MTSL C10 H18 N O3 S2 MXZPGYFBZHBAQM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.216 
• R-Value Work: 0.171 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 60.657	α = 90.00
b = 60.657	β = 90.00
c = 96.448	γ = 120.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
DENZO	data reduction
PDB_EXTRACT	data extraction
CrystalClear	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-02-02 
• Released Date: 2009-05-05 
• Deposition Author(s): Fleissner, M.R., Cascio, D., Hubbell, W.L.

Revision History 

• Version 1.0: 2009-05-05
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2011-07-27
  Type: Non-polymer description
• Version 1.3: 2017-11-01
  Type: Advisory, Refinement description