3KLR

Bovine H-protein at 0.88 angstrom resolution

Summary for 3KLR

• Entry DOI: 10.2210/pdb3klr/pdb
• Descriptor: Glycine cleavage system H protein, SULFATE ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: antiparallel beta sheet, beta sandwich, oxidoreductase
• Biological source: Bos taurus (bovine)
• Cellular location: Mitochondrion : P20821
• Total number of polymer chains: 1
• Total formula weight: 14142.59

Authors

Higashiura, A.,Kurakane, T.,Matsuda, M.,Suzuki, M.,Inaka, K.,Sato, M.,Tanaka, H.,Fujiwara, K.,Nakagawa, A. (deposition date: 2009-11-09, release date: 2010-06-09, Last modification date: 2023-11-01)

Primary citation

Higashiura, A.,Kurakane, T.,Matsuda, M.,Suzuki, M.,Inaka, K.,Sato, M.,Kobayashi, T.,Tanaka, T.,Tanaka, H.,Fujiwara, K.,Nakagawa, A.
High-resolution X-ray crystal structure of bovine H-protein at 0.88 A resolution
Acta Crystallogr.,Sect.D, 66:698-708, 2010

PubMed Abstract: Recent technical improvements in macromolecular X-ray crystallography have significantly improved the resolution limit of protein structures. However, examples of high-resolution structure determination are still limited. In this study, the X-ray crystal structure of bovine H-protein, a component of the glycine cleavage system, was determined at 0.88 A resolution. This is the first ultrahigh-resolution structure of an H-protein. The data were collected using synchrotron radiation. Because of limitations of the hardware, especially the dynamic range of the CCD detector, three data sets (high-, medium- and low-resolution data sets) were measured in order to obtain a complete set of data. To improve the quality of the merged data, the reference data set was optimized for merging and the merged data were assessed by comparing merging statistics and R factors against the final model and the number of visualized H atoms. In addition, the advantages of merging three data sets were evaluated. The omission of low-resolution reflections had an adverse effect on visualization of H atoms in hydrogen-omit maps. Visualization of hydrogen electron density is a good indicator for assessing the quality of high-resolution X-ray diffraction data.

PubMed: 20516622
DOI: 10.1107/S0907444910010668

Experimental method

X-RAY DIFFRACTION (0.88 Å)