Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.36 kDa 
• Atom Count: 1047 
• Residue Count: 129 
• Unique protein chains: 1

2YBM

Nitrate X-ray induced reduction on HEWL crystals (23.3 MGy)

• DOI: 10.2210/pdb2YBM/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2011-03-08 Released: 2011-07-20 
• Deposition Author(s): De la Mora, E., Carmichael, I., Garman, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.242 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Literature

Effective Scavenging at Cryotemperatures: Further Increasing the Dose Tolerance of Protein Crystals.

De La Mora, E., Carmichael, I., Garman, E.F.

(2011) J Synchrotron Radiat 18: 346

• PubMed: 21525642 
• DOI: 10.1107/S0909049511007163
• Primary Citation of Related Structures:  
  2YBL, 2YBM, 2YBN, 2YBH, 2YBI, 2YBJ, 2YDG


• PubMed Abstract: 
  

The rate of radiation damage to macromolecular crystals at both room temperature and 100 K has previously been shown to be reduced by the use of certain radical scavengers. Here the effects of sodium nitrate, an electron scavenger, are investigated at 100 K. For sodium nitrate at a concentration of 0.5 M in chicken egg-white lysozyme crystals, the dose tolerance is increased by a factor of two as judged from the global damage parameters, and no specific structural damage to the disulfide bonds is seen until the dose is greatly in excess (more than a factor of five) of the value at which damage appears in electron density maps derived from a scavenger-free crystal. In the electron density maps, ordered nitrate ions adjacent to the disulfide bonds are seen to lose an O atom, and appear to protect the disulfide bonds. In addition, results reinforcing previous reports on the effectiveness of ascorbate are presented. The mechanisms of action of both scavengers in the crystalline environment are elucidated.

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME C	A	129	Gallus gallus	Mutation(s): 0  Gene Names: LYZ EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO	A	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYAM

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.242 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.2	α = 90
b = 78.2	β = 90
c = 38.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-03-08 
• Released Date: 2011-07-20 
Deposition Author(s): De la Mora, E., Carmichael, I., Garman, E.F.

Revision History 

• Version 1.0: 2011-07-20
  Type: Initial release