8WXP image
Deposition Date 2023-10-30
Release Date 2023-11-22
Last Version Date 2024-11-13
Entry Detail
PDB ID:
8WXP
Title:
Crystal structure of substrate-binding protein from Rhodothermus marinus (Dose IV)
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.75 Å
R-Value Free:
0.27
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:ABC-type uncharacterized transport system periplasmic component-like protein
Gene (Uniprot):Rmar_2176
Chain IDs:A, B
Chain Length:164
Number of Molecules:2
Biological Source:Rhodothermus marinus DSM 4252
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MSE A MET modified residue
Primary Citation
Data of radiation damage on selenomethionine-substituted single-domain substrate-binding protein.
Data Brief 53 110114 110114 (2024)
PMID: 38348329 DOI: 10.1016/j.dib.2024.110114

Abstact

Radiation damage is an inherent issue in X-ray crystallography. It not only damages macromolecular crystals, which lowers the quality of the diffraction intensity, but results in inaccurate structural information. Among the various types of radiation damage, little is known regarding the damage to selenomethionine, an amino acid contained in some proteins. Recently, radiation damage to the selenomethionine-substituted single-domain substrate-binding domain from Rhodothermus marinus (SeMet-RmSBP) was investigated. Global and specific radiation damage from four datasets collected by repeatedly exposing a single RmSBP-SeMet crystal to X-rays were analyzed. The results indicated that the B-factor value of the selenium atom in selenomethionine was significantly increased compared with other atoms. To date, no images of radiation damage have been reported for selenomethionine-substituted proteins. Therefore, these data may be used to study radiation damage in macromolecular crystallography. This study provides insight into radiation damage associated with selenomethionine.

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Primary Citation of related structures