Rationalizing the Geometries of the Water Oxidising Complex in the Atomic Resolution, Nominal S 3 State Crystal Structures of Photosystem II

ChemPhysChem ◽  
2020 ◽  
Vol 21 (8) ◽  
pp. 785-801 ◽  
Author(s):  
Simon Petrie ◽  
Richard Terrett ◽  
Robert Stranger ◽  
Ron J. Pace
Keyword(s):  
Photosystem Ii ◽  
Crystal Structures ◽  
Atomic Resolution

Atomic resolution crystal structures of HIV-1 protease and mutants V82A and I84V with saquinavir

2007 ◽  
Vol 67 (1) ◽  
pp. 232-242 ◽  
Author(s):  
Yunfeng Tie ◽  
Andrey Y. Kovalevsky ◽  
Peter Boross ◽  
Yuan-Fang Wang ◽  
Arun K. Ghosh ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Atomic Resolution ◽  
Hiv 1

Use of Patterson-based methods automatically to determine the structures of heavy-atom-containing proteins with up to 6000 non-hydrogen atoms in the asymmetric unit

2006 ◽  
Vol 39 (5) ◽  
pp. 728-734 ◽  
Author(s):  
Maria Cristina Burla ◽  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Liberato De Caro ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Protein Data Bank ◽  
Heavy Atom ◽  
Data Bank ◽  
Atomic Resolution ◽  
Asymmetric Unit ◽  
Hydrogen Atoms ◽  
Heavy Atoms ◽  
Density Maps ◽  
Resolution Data

The Patterson superposition methods described by Burlaet al.[J. Appl. Cryst.(2006),39, 527–535], based on the use of the `multiple implication functions', have been enriched by supplementary filtering techniques based on some general (resolution-dependent) features of both the Patterson and the electron density maps. The method has been implemented in a modified version of the programSIR2004and tested using a set of 20 crystal structures selected from the Protein Data Bank, having a number of non-hydrogen atoms in the asymmetric unit larger than 2000, atomic resolution data and some heavy atoms (equal to or heavier than Ca). The new phasing procedure is able to solve most of the test structures, among which there are two proteins with more than 6000 non-hydrogen atoms in the asymmetric unit, so extending by far the complexity today commonly considered as the limit for Patterson-based methods (i.e.about 2000 non-hydrogen atoms).

scholarly journals Structure determination from X-ray powder diffraction data at low resolution

2014 ◽  
Vol 70 (a1) ◽  
pp. C143-C143
Author(s):  
Hongliang Xu
Keyword(s):  
Single Crystal ◽  
Diffraction Pattern ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Direct Methods ◽  
Atomic Resolution ◽  
Powder Diffraction Data ◽  
Low Resolution

Knowledge of the structural arrangement of atoms in solids is necessary to facilitate the study of their properties. The best and most detailed structural information is obtained when the diffraction pattern of a single crystal a few tenths of a millimeter in each dimension is analyzed, but growing high-quality crystals of this size is often difficult, sometimes impossible. However, many crystallization experiments that do not yield single crystals do yield showers of randomly oriented micro-crystals that can be exposed to X-rays simultaneously to produce a powder diffraction pattern. Direct Methods routinely solve crystal structures when single-crystal diffraction data are available at atomic resolution (1.0-1.2Å), but fail to determine micro-crystal structures due to reflections overlapping and low-resolution powder diffraction data. By artificially and intelligently extending the measured data to atomic resolution, we have successfully solved structures having low-resolution diffraction data that were hard to solve by other direct-method based computation procedures. The newly developed method, Powder Shake-and-Bake, is implemented in a computer program PowSnB. PowSnB can be incorporated into the state-of-the-art software package EXPO that includes powder data reduction, structure determination and structure refinement. The new combination could have potential to solve structures that have never been solved before by direct-methods approach.

2L1412 Crystal structure of oxygen evolving Photosystem II complex at an atomic resolution(Photobiology: Photosynthesis,The 48th Annual Meeting of the Biophysical Society of Japan)

2011 ◽  
Vol 51 (supplement) ◽  
pp. S95
Author(s):  
Yasufumi Umena ◽  
Keisuke Kawakami ◽  
Nobuo Kamiya ◽  
Jian-Ren Shen
Keyword(s):  
Crystal Structure ◽  
Photosystem Ii ◽  
Annual Meeting ◽  
Atomic Resolution ◽  
Biophysical Society ◽  
Oxygen Evolving

scholarly journals Ligand Binding Induces Conformational Changes in Human Cellular Retinol-binding Protein 1 (CRBP1) Revealed by Atomic Resolution Crystal Structures

2016 ◽  
Vol 291 (16) ◽  
pp. 8528-8540 ◽  
Author(s):  
Josie A. Silvaroli ◽  
Jason M. Arne ◽  
Sylwia Chelstowska ◽  
Philip D. Kiser ◽  
Surajit Banerjee ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Crystal Structures ◽  
Conformational Changes ◽  
Binding Protein ◽  
Retinol Binding Protein ◽  
Atomic Resolution ◽  
Cellular Retinol Binding Protein

scholarly journals Atomic-resolution crystal structures of the immune protein conglutinin from cow reveal specific interactions of its binding site with N-acetylglucosamine

2019 ◽  
Vol 294 (45) ◽  
pp. 17155-17165
Author(s):  
Janet M. Paterson ◽  
Amy J. Shaw ◽  
Ian Burns ◽  
Alister W. Dodds ◽  
Alpana Prasad ◽  
...  
Keyword(s):  
Binding Site ◽  
Crystal Structures ◽  
Atomic Resolution ◽  
Specific Interactions

scholarly journals Archaeal actin from a hyperthermophile forms a single-stranded filament

2015 ◽  
Vol 112 (30) ◽  
pp. 9340-9345 ◽  
Author(s):  
Tatjana Braun ◽  
Albina Orlova ◽  
Karin Valegård ◽  
Ann-Christin Lindås ◽  
Gunnar F. Schröder ◽  
...  
Keyword(s):  
Actin Cytoskeleton ◽  
Crystal Structures ◽  
Actin Filaments ◽  
Phylogenetic Analyses ◽  
Atomic Resolution ◽  
Electron Cryomicroscopy ◽  
Large Variability ◽  
Sequence Identity ◽  
Subunit Interface ◽  
Large Insertion

The prokaryotic origins of the actin cytoskeleton have been firmly established, but it has become clear that the bacterial actins form a wide variety of different filaments, different both from each other and from eukaryotic F-actin. We have used electron cryomicroscopy (cryo-EM) to examine the filaments formed by the protein crenactin (a crenarchaeal actin) from Pyrobaculum calidifontis, an organism that grows optimally at 90 °C. Although this protein only has ∼20% sequence identity with eukaryotic actin, phylogenetic analyses have placed it much closer to eukaryotic actin than any of the bacterial homologs. It has been assumed that the crenactin filament is double-stranded, like F-actin, in part because it would be hard to imagine how a single-stranded filament would be stable at such high temperatures. We show that not only is the crenactin filament single-stranded, but that it is remarkably similar to each of the two strands in F-actin. A large insertion in the crenactin sequence would prevent the formation of an F-actin-like double-stranded filament. Further, analysis of two existing crystal structures reveals six different subunit–subunit interfaces that are filament-like, but each is different from the others in terms of significant rotations. This variability in the subunit–subunit interface, seen at atomic resolution in crystals, can explain the large variability in the crenactin filaments observed by cryo-EM and helps to explain the variability in twist that has been observed for eukaryotic actin filaments.

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