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Successful data recovery from oscillation photographs containing strong polycrystalline diffraction rings from an unknown small‐molecule contaminant: preliminary structure solution of Salmonella typhimurium pyridoxal kinase (PdxK)
Author(s) -
Deka G.,
Kalyani J. N.,
Benazir J. F.,
Savithri H. S.,
Murthy M. R. N.
Publication year - 2014
Publication title -
acta crystallographica section f
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.572
H-Index - 37
ISSN - 2053-230X
DOI - 10.1107/s2053230x14005342
Subject(s) - pyridoxal , orthorhombic crystal system , protein data bank (rcsb pdb) , crystallography , molecular replacement , chemistry , kinase , crystal structure , stereochemistry , enzyme , biochemistry
Pyridoxal kinase (PdxK; EC 2.7.1.35) belongs to the phosphotransferase family of enzymes and catalyzes the conversion of the three active forms of vitamin B 6 , pyridoxine, pyridoxal and pyridoxamine, to their phosphorylated forms and thereby plays a key role in pyridoxal 5′‐phosphate salvage. In the present study, pyridoxal kinase from Salmonella typhimurium was cloned and overexpressed in Escherichia coli , purified using Ni–NTA affinity chromatography and crystallized. X‐ray diffraction data were collected to 2.6 Å resolution at 100 K. The crystal belonged to the primitive orthorhombic space group P 2 1 2 1 2 1 , with unit‐cell parameters a = 65.11, b = 72.89, c = 107.52 Å. The data quality obtained by routine processing was poor owing to the presence of strong diffraction rings caused by a polycrystalline material of an unknown small molecule in all oscillation images. Excluding the reflections close to powder/polycrystalline rings provided data of sufficient quality for structure determination. A preliminary structure solution has been obtained by molecular replacement with the Phaser program in the CCP 4 suite using E. coli pyridoxal kinase (PDB entry 2ddm ) as the phasing model. Further refinement and analysis of the structure are likely to provide valuable insights into catalysis by pyridoxal kinases.