4REK

Crystal structure and charge density studies of cholesterol oxidase from Brevibacterium sterolicum at 0.74 ultra-high resolution

Summary for 4REK

• Entry DOI: 10.2210/pdb4rek/pdb
• Related: 1N1P
• Descriptor: Cholesterol oxidase, FLAVIN-ADENINE DINUCLEOTIDE, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: oxidase, fad binding, membrane, oxidoreductase
• Biological source: Streptomyces sp.
• Cellular location: Secreted: P12676
• Total number of polymer chains: 1
• Total formula weight: 55405.80

Authors

Zarychta, B.,Lyubimov, A.,Ahmed, M.,Munshi, P.,Guillot, B.,Vrielink, A. (deposition date: 2014-09-23, release date: 2015-04-15, Last modification date: 2023-09-20)

Primary citation

Zarychta, B.,Lyubimov, A.,Ahmed, M.,Munshi, P.,Guillot, B.,Vrielink, A.,Jelsch, C.
Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis.
Acta Crystallogr.,Sect.D, 71:954-968, 2015

PubMed Abstract: Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiation to an optical resolution of 0.94 Å. After refinement using the spherical atom model, nonmodelled bonding peaks were detected in the Fourier residual electron density on some of the individual bonds. Well defined bond density was observed in the peptide plane after averaging maps on the residues with the lowest thermal motion. The multipolar electron density of the protein-cofactor complex was modelled by transfer of the ELMAM2 charge-density database, and the topology of the intermolecular interactions between the protein and the flavin adenine dinucleotide (FAD) cofactor was subsequently investigated. Taking advantage of the high resolution of the structure, the stereochemistry of main-chain bond lengths and of C=O···H-N hydrogen bonds was analyzed with respect to the different secondary-structure elements.

PubMed: 25849405
DOI: 10.1107/S1399004715002382

Experimental method

X-RAY DIFFRACTION (0.74 Å)