ISDA: 2YBM

Deposition Date 2011-03-08

Release Date 2011-07-20

Last Version Date 2024-11-13

Entry Detail

PDB ID:

2YBM

Keywords:

HYDROLASE

Title:

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

Biological Source:

Source Organism:

GALLUS GALLUS (Taxon ID: 9031)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.00 Å

R-Value Free:

0.24

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 43 21 2

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:LYSOZYME C
Gene (Uniprot):LYZ
Chain IDs:A
Chain Length:129
Number of Molecules:1
Biological Source:GALLUS GALLUS

UniProt ID:P00698 Pfam ID:PF00062 EC:3.2.1.17

Ligand Molecules

Primary Citation

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

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

J.Synchrotron.Radiat. 18 346 ? (2011)

PMID: 21525642 DOI: 10.1107/S0909049511007163

Abstact

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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