Dataset Information

The Shake-and-Bake structure determination of triclinic lysozyme.

ABSTRACT: The crystal structure of triclinic lysozyme, comprised of 1,001 non-H protein atoms and approximately 200 bound water molecules, has been determined ab initio (using native data alone) by the "Shake-and-Bake" method by using the computer program SnB. This is the largest structure determined so far by the SnB program. Initial experiments, using default SnB parameters derived from studies of smaller molecules, were unsuccessful. In fact, such experiments produced electron density maps dominated by a single large peak. This problem was overcome by considering the choice of protocol used during the parameter-shift phase refinement. When each phase was subjected to a single shift of +/-157.5 degrees during each SnB cycle, an unusually high percentage of random trials (approximately 22%) yielded correct solutions within 750 cycles. This success rate is higher than that typically observed, even for much smaller structures.

SUBMITTER: Deacon AM

PROVIDER: S-EPMC21330 | biostudies-literature | 1998 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

The Shake-and-Bake structure determination of triclinic lysozyme.

Deacon A M AM Weeks C M CM Miller R R Ealick S E SE

Proceedings of the National Academy of Sciences of the United States of America 19980801 16

The crystal structure of triclinic lysozyme, comprised of 1,001 non-H protein atoms and approximately 200 bound water molecules, has been determined ab initio (using native data alone) by the "Shake-and-Bake" method by using the computer program SnB. This is the largest structure determined so far by the SnB program. Initial experiments, using default SnB parameters derived from studies of smaller molecules, were unsuccessful. In fact, such experiments produced electron density maps dominated by ...[more]

PMID: 9689072

Similar Datasets

Project description:BackgroundPoly(?-glutamic acid) (?-PGA) is a biopolymer with many useful properties making it applicable for instance in food and skin care industries, in wastewater treatment, in biodegradable plastics or in the pharmaceutical industry. ?-PGA is usually produced microbially by different Bacillus spp. The produced ?-PGA increases the viscosity of the fermentation broth. In case of shake flask fermentations, this results in an increase of the volumetric power input. The power input in shake flasks can be determined by measuring the torque of an orbitally rotating lab shaker. The online measurement of the volumetric power input enables to continuously monitor the formation or degradation of viscous products like ?-PGA. Combined with the online measurement of the oxygen transfer rate (OTR), the respiration activity of the organisms can be observed at the same time.ResultsTwo different Bacillus licheniformis strains and three medium compositions were investigated using online volumetric power input and OTR measurements as well as thorough offline analysis. The online volumetric power input measurement clearly depicted changes in ?-PGA formation due to different medium compositions as well as differences in the production behavior of the two investigated strains. A higher citric acid concentration and the addition of trace elements to the standard medium showed a positive influence on ?-PGA production. The online power input signal was used to derive an online viscosity signal which was validated with offline determined viscosity values. The online measurement of the OTR proved to be a valuable tool to follow the respiration activity of the cultivated strains and to determine its reproducibility under different cultivation conditions.ConclusionsThe combination of the volumetric power input and the OTR allows for an easy and reliable investigation of new strains, cultivation conditions and medium compositions for their potential in ?-PGA production. The power input signal and the derived online viscosity directly reflect changes in ?-PGA molecular weight and concentration, respectively, due to different cultivation conditions or production strains.

Dataset Information

The Shake-and-Bake structure determination of triclinic lysozyme.

Publications

The Shake-and-Bake structure determination of triclinic lysozyme.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure