PDBsum entry 1dwh

Hydrolase

PDB id: 1dwh

Contents

Protein chain

499 a.a. *

Ligands

NAG-NAG ×2

NAG-NAG-BMA-XYP-FUC

NAG-NAG-BMA-XYP-MAN-MAN-FUC

NAG ×6

SO4 ×8

GOL ×5

Metals

_ZN

Waters ×788

* Residue conservation analysis

PDB id:

1dwh

Name:

Hydrolase

Title:

Study on radiation damage on a cryocooled crystal. Part 4: structure after irradiation with 27.2 10E15 photons/mm2

Structure:

Myrosinase ma1. Chain: m. Fragment: residues 3-501. Synonym: thioglucoside glucohydrolase, sinigrinase, thioglucosidase. Other_details: after irradiation with 27.2 10E15 photons/ mm2

Source:

Sinapis alba. White mustard. Organism_taxid: 3728. Strain: emergo. Organ: seed. Cell: myrosin cells. Cellular_location: myrosin grains

Resolution:

2.00Å R-factor: 0.205 R-free: 0.217

Authors:

W.P.Burmeister

Key ref:

W.P.Burmeister (2000). Structural changes in a cryo-cooled protein crystal owing to radiation damage. Acta Crystallogr D Biol Crystallogr, 56, 328-341. PubMed id: 10713520 DOI: 10.1107/S0907444999016261

Date:

05-Dec-99 Release date: 03-Mar-00

Protein chain

P29736  (MYRA_SINAL) -  Myrosinase MA1 from Sinapis alba

Seq: 501 a.a.

Struc: 499 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.2.1.147 - thioglucosidase.
• Reaction: a thioglucoside + H2O = a sugar + a thiol

thioglucoside (Bound ligand (Het Group name = BMA) matches with 84.62% similarity) + H2O = sugar + thiol

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1107/S0907444999016261

Acta Crystallogr D Biol Crystallogr 56:328-341 (2000)

PubMed id: 10713520

Structural changes in a cryo-cooled protein crystal owing to radiation damage.

W.P.Burmeister.

ABSTRACT

The high intensity of third-generation X-ray sources, along with the development of cryo-cooling of protein crystals at temperatures around 100 K, have made it possible to extend the diffraction limit of crystals and to reduce their size. However, even with cryo-cooled crystals, radiation damage becomes a limiting factor. So far, the radiation damage has manifested itself in the form of a loss of overall diffracted intensity and an increase in the temperature factor. The structure of a protein (myrosinase) after exposure to different doses of X-rays in the region of 20 x 10(15) photons mm(-2) has been studied. The changes in the structure owing to radiation damage were analysed using Fourier difference maps and occupancy refinement for the first time. Damage was obvious in the form of breakage of disulfide bonds, decarboxylation of aspartate and glutamate residues, a loss of hydroxyl groups from tyrosine and of the methylthio group of methionine. The susceptibility to radiation damage of individual groups of the same kind varies within the protein. The quality of the model resulting from structure determination might be compromised owing to the presence of radiolysis in the crystal after an excessive radiation dose. Radiation-induced structural changes may interfere with the interpretation of ligand-binding studies or MAD data. The experiments reported here suggest that there is an intrinsic limit to the amount of data which can be extracted from a sample of a given size.

Selected figure(s)

Figure 1.
Figure 1 Radical reactions caused by X-ray or electron irradiation which are likely to contribute to the observed radiation damage to the amino-acid side chains. (p)- represents protein. References for the reactions are given in the text. The mechanism for reaction (5) is not known; only the products have been identified (Schimazu et al., 1964[Berthet-Colominas, C., Monaco, S., Novelli, A., Sibaï, G., Mallet, F. & Cusack, S. (1999). EMBO J. 18, 1124-1136.]).

Figure 5.
Figure 5 Individually refined occupancies of labile groups. The most rapid loss of electron density (plotted with squares, residue name given) is fitted with an exponential function (dotted line). The rate constants obtained from these fits are given in Table 2-; the scatter of the points gives an idea of the statistical errors of the refined occupancies. The groups shown in Fig. 3-are plotted as black squares. (a) S atoms of free cysteines (dashed lines) and disulfide bridges (solid lines). (b) Carboxyl groups of glutamic acid residues. (c) Carboxyl groups of aspartate residues. For clarity, the connecting lines are only drawn for every fifth residue. Asp70 (triangles) is involved in the coordination of the Zn atom. (d) Hydroxyl groups of tyrosine. For clarity, the connecting lines are only drawn for every fifth residue. (e) Methylthio groups of methionine.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2000, 56, 328-341) copyright 2000.

Figures were selected by an automated process.