Bilirubin oxidase from Myrothecium verrucaria: X-ray determination of the complete crystal structure and a rational surface modification for enhanced electrocatalytic O2 reduction

X-ray irradiation on a protein crystal can cause some subtle structural modification on the protein structure even if the radiation dose is much smaller than a dose used for a common crystal structure determination. In some case such structural modification increases ambiguity of structural inspection, and eventually could be an obstacle on the elucidation of structure basis of protein function. Bovine heart cytochrome c oxidase (CcO) is one of such proteins having some problem caused by the radiation damage. The proton pumping of CcO is coupled with O2 reduction at the O2 reduction site, thus accurate structure determination of bound ligand as well as CcO itself is very important. Whereas accurate structure determination was impeded by the immediate photolysis of the peroxide ligand upon X-ray irradiation even at a cryogenic temperature[1]. We developed a goniometer based data collection system for the femtosecond crystallography at SACLA (SPring-8 Angstrom Compact free-electron LAser). The femtosecond crystallography is expected to have an advantage in high-resolution and radiation damage free structure determination of very large protein by combined usage of large crystal and femtosecond intense X-ray pulse. In this presentation we are going to show the result of the femtosecond crystallography on the crystal of CcO having large unit cell dimensions. The close inspection of the electron density map calculated at 1.9 Å resolution showed the femtosecond crystallography worked fine for the high resolution and radiation damage free crystal structure determination of CcO.

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Single Crystal Growth of High-Pressure Phases of Ice and Salt Hydrate Far Below the Original Melting Point by Mixing Alcohol: Crystal Structure Determination of Magnesium Chloride Heptahydrate

10.26434/chemrxiv.11345063.v2 ◽

2020 ◽

Author(s):

Keishiro Yamashita ◽

Kazuki Komatsu ◽

Hiroyuki Kagi

Keyword(s):

Crystal Structure ◽

High Pressure ◽

Crystal Growth ◽

Single Crystal ◽

Room Temperature ◽

Growth Technique ◽

Salt Hydrate ◽

X Ray

An crystal-growth technique for single crystal x-ray structure analysis of high-pressure forms of hydrogen-bonded crystals is proposed. We used alcohol mixture (methanol: ethanol = 4:1 in volumetric ratio), which is a widely used pressure transmitting medium, inhibiting the nucleation and growth of unwanted crystals. In this paper, two kinds of single crystals which have not been obtained using a conventional experimental technique were obtained using this technique: ice VI at 1.99 GPa and MgCl<sub>2</sub>·7H<sub>2</sub>O at 2.50 GPa at room temperature. Here we first report the crystal structure of MgCl2·7H2O. This technique simultaneously meets the requirement of hydrostaticity for high-pressure experiments and has feasibility for further in-situ measurements.

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The protonation of the ethylenediphosphinetetraacetate anion and the crystal structure of the bis (hydrogen bromide) of ethylenediphosphinetetraacetic acid

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19813063 ◽

1981 ◽

Vol 46 (12) ◽

pp. 3063-3073 ◽

Cited By ~ 5

Author(s):

Jana Podlahová ◽

Bohumil Kratochvíl ◽

Vratislav Langer ◽

Josef Šilha ◽

Jaroslav Podlaha

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Structure Determination ◽

Free Acid ◽

Hydrogen Bromide ◽

Carboxyl Groups ◽

Spectroscopic Methods ◽

X Ray ◽

Partial Formation

The equilibria and mechanism of addition of protons to the ethylenediphosphinetetraacetate anion (L4-) were studied in solution by the UV, IR, 1H and 31P NMR spectroscopic methods. A total of six protons can be bonded to the anion. They are added stepwise, first with partial formation of zwitterions containing P-H bonds, which then dissociate with formation of the free acid, H4L, where all four protons are bonded in carboxyl groups. The formation of zwitterions is strongly dependent on the concentration. In the final stage, the acid bonds two additional protons to form the bis-phosphonium cation, H6L2+. A number of isostructural salts containing this cation, H4L.2 HX (X = Cl, Br, I), have been prepared. The X-ray crystal structure determination of the bromide confirmed the expected arrangement. The bromide crystals are monoclinic, a = 578.2, b = 1 425.0, c = 1 046.7 pm, β = 103.07° with a space group of P21/c, Z = 2. The final R factor was 0.059 based on 1 109 observed reflections. The structure consists of H6L2+ cations containing protons bonded to phosphorus atoms (P-H distance 134 pm) and of bromide anions, located in gaps which are also sufficiently large for I- anions in the isostructural iodide. The interbonding of phosphonium cations proceeds through hydrogen bonds, C-OH...O=C, in which the O...O distance is 275.3 pm.

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Crystal structure determination of the conformation of two bicyclo[3.3.1]nonan-ones

Canadian Journal of Chemistry ◽

10.1139/v85-198 ◽

1985 ◽

Vol 63 (6) ◽

pp. 1166-1169 ◽

Cited By ~ 4

Author(s):

John F. Richardson ◽

Ted S. Sorensen

Keyword(s):

Crystal Structure ◽

Direct Methods ◽

Chair Conformation ◽

Molecular Structures ◽

Boat Conformation ◽

X Ray Diffraction ◽

Space Group ◽

X Ray ◽

Final Agreement

The molecular structures of exo-7-methylbicyclo[3.3.1]nonan-3-one, 3, and the endo-7-methyl isomer, 4, have been determined using X-ray-diffraction techniques. Compound 3 crystallizes in the space group [Formula: see text] with a = 15.115(1), c = 7.677(2) Å, and Z = 8 while 4 crystallizes in the space group P21 with a = 6.446(1), b = 7.831(1), c = 8.414(2) Å, β = 94.42(2)°, and Z = 2. The structures were solved by direct methods and refined to final agreement factors of R = 0.041 and R = 0.034 for 3 and 4 respectively. Compound 3 exists in a chair–chair conformation and there is no significant flattening of the chair rings. However, in 4, the non-ketone ring is forced into a boat conformation. These results are significant in interpreting what conformations may be present in the related sp2-hybridized carbocations.

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Preparative-scale HPLC Resolution of Metallacyclic η3-Allyltricarbonyliron Complexes and Determination of the Absolute Configuration by X-Ray Crystal Structure Analysis

Journal of Chemical Research ◽

10.1177/174751989902300930 ◽

1999 ◽

Vol 23 (9) ◽

pp. 578-579

Author(s):

Rainer Schobert ◽

Hermann Pfab ◽

Jutta Böhmer ◽

Frank Hampel ◽

Andreas Werner

Keyword(s):

Crystal Structure ◽

Silica Gel ◽

Structure Analysis ◽

Absolute Configuration ◽

Crystal Structure Analysis ◽

Preparative Scale ◽

X Ray ◽

The Absolute

Racemates of (η3-allyl)tricarbonyliron lactone complex Fe(CO)3{η1:η3-C(O)XCH2CHCMeCH2} 1a (X = O) and (η3-allyl)tricarbonyliron lactam complex 2a (X = NMe) are resolved on a preparative scale by HPLC on cellulose tris(3,5-dimethylphenyl)carbamate/silica gel RP-8 and the absolute configuration of (-)-2a is determined by X-ray crystal structure analysis.

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