scholarly journals Crystal structure of fibrinogen-Aα peptide 1–23 (F8Y) bound to bovine thrombin explains why the mutation of Phe-8 to tyrosine strongly inhibits normal cleavage at Arg-16

1997 ◽  
Vol 326 (3) ◽  
pp. 815-822 ◽  
Author(s):  
Michael G. MALKOWSKI ◽  
Philip D. MARTIN ◽  
Susan T. LORD ◽  
Brian F. P. EDWARDS
Keyword(s):  
Crystal Structure ◽  
Structural Basis ◽  
Side Chain ◽  
Asymmetric Unit ◽  
Bovine Thrombin ◽  
R Factor ◽  
Native Peptide ◽  
Cell Dimensions ◽  
Scissile Bond ◽  
Unit Cell Dimensions

A peptide containing residues 1–50 of the Aα-chain of fibrinogen, expressed as a fusion peptide with β-galactosidase, is rapidly cleaved by thrombin at Arg-16, similarly to whole fibrinogen. When Phe-8, which is highly conserved, is replaced with tyrosine (F8Y), the cleavage is slowed drastically [Lord, Byrd, Hede, Wei and Colby (1990) J. Biol. Chem. 265, 838–843]. To examine the structural basis for this result, we have determined the crystal structure of bovine thrombin complexed with a synthetic peptide containing residues 1–23 of fibrinogen Aα and the F8Y mutation. The crystals are in space group P43212, with unit-cell dimensions of a = 88.3 Å (1 Å = 0.1 nm), c = 195.5 Å and two complexes in the asymmetric unit. The final R factor is 0.183 for 2σ data from 7.0 to 2.5 Å resolution. There is continuous density for the five residues in the P3, P2, P1, P1′ and P2′ positions of the peptide (Gly-14f to Pro-18f) at the active site of thrombin, and isolated but well-defined density for Tyr-8f at position P9 in the hydrophobic pocket of thrombin. The tyrosine residue is shifted relative to phenylalanine in the native peptide because the phenol side chain is larger and makes a novel, intrapeptide hydrogen bond with Gly-14f. Adjacent peptide residues cannot form the hydrogen bonds that stabilize the secondary structure of the native peptide. Consequently, the ‘reaction’ geometry at the scissile bond, eight residues from the mutation, is perturbed and the peptide is mostly uncleaved in the crystal structure.

Appendix. Crystallographic measurements on the anti-pernicious anaemia factor

1950 ◽  
Vol 136 (885) ◽  
pp. 609-613 ◽  
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Pernicious Anaemia ◽  
Aqueous Acetone ◽  
Crystal Habit ◽  
Side Chain ◽  
Solvent Content ◽  
X Ray ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

Since May 1948, five different samples of crystalline anti-pernicious anaemia factor have been examined in Oxford by various crystallographic techniques. These all, from their general characteristics, particularly the intensities of a number of X-ray reflexions, contain the same molecular structure. But the different samples have shown small variations in unit-cell dimensions and in crystal habit, which are probably due mainly to differences in solvent content, combined with traces of different impurities. Small changes in, for example, some side chain in the molecule, might also conceivably contribute to these effects. The crystals, as grown both from water and from aqueous acetone, are dark red and show marked pleochroism . They vary in habit from long thin needles to short thick prisms on which different crystal faces appear (figures A 1 and A 2). They all contain solvent, probably water, of crystallization, part at least of which they lose slowly on exposure to the air. Crystals kept in their mother-liquor are transparent and show beautifully clear reflecting faces; they give sharp X-ray reflexions extending to spacings of 1·1Å. On removal from the liquid they tend to crack and to become opaque; the faces are distorted and the X-ray reflexions become first multiple, and then blurred, corresponding to the presence of disorder within the dried crystal structure. But the rate of loss of solvent appears to vary both with the size of crystals and with the different samples studied. Individual air-dried crystals for example, have been observed which have given good and sharp X-ray reflexions some weeks after exposure to the atmosphere.

The structure of plastocyanin from the cyanobacterium Phormidium laminosum

1999 ◽  
Vol 55 (2) ◽  
pp. 414-421 ◽  
Author(s):  
Charles S. Bond ◽  
Derek S. Bendall ◽  
Hans C. Freeman ◽  
J. Mitchell Guss ◽  
Christopher J. Howe ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Search Model ◽  
Molecular Replacement ◽  
Amino Acid Residues ◽  
Asymmetric Unit ◽  
Threefold Axis ◽  
Phormidium Laminosum ◽  
X Ray ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

The crystal structure of the `blue' copper protein plastocyanin from the cyanobacterium Phormidium laminosum has been solved and refined using 2.8 Å X-ray data. P. laminosum plastocyanin crystallizes in space group P43212 with unit-cell dimensions a = 86.57, c = 91.47 Å and with three protein molecules per asymmetric unit. The final residual R is 19.9%. The structure was solved using molecular replacement with a search model based on the crystal structure of a close homologue, Anabaena variabilis plastocyanin (66% sequence identity). The molecule of P. laminosum plastocyanin has 105 amino-acid residues. The single Cu atom is coordinated by the same residues – two histidines, a cysteine and a methionine – as in other plastocyanins. In the crystal structure, the three molecules of the asymmetric unit are related by a non-crystallographic threefold axis. A Zn atom lies between each pair of neighbouring molecules in this ensemble, being coordinated by a surface histidine residue of one molecule and by two aspartates of the other.

The Crystal Structure of a Thiathiophthen Nitrogen Isostere, 3,5-Epidithio-2,5-diphenyl-2,4-pentadienylidene-3-aminoquinoline

1971 ◽  
Vol 49 (2) ◽  
pp. 167-172 ◽  
Author(s):  
F. Leung ◽  
S. C. Nyburg
Keyword(s):  
Crystal Structure ◽  
Least Squares ◽  
Unit Cell ◽  
Full Matrix ◽  
X Ray ◽  
Bond Lengths ◽  
Triclinic System ◽  
R Factor ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

The crystal structure of a thiathiophthen nitrogen isostere (7) has been solved by X-ray analysis. The crystal belongs to the triclinic system with unit cell dimensions: a = 11.275(11), b = 9.558(10), c = 10.797(10) Å, α = 92.50(10), β = 116.98(10), γ = 92.61(10)°. There are two molecules per unit cell, space group [Formula: see text]. The data were collected by diffractometer with CuKα radiation. The structure was solved by symbolic addition procedures, and fully refined anisotropically using full-matrix least squares to an R factor of 6.3%.The S—S and S—N bond lengths were found to be 2.364 and 1.887 Å, respectively. This reveals the partial bonding character between S … S … N atoms.

scholarly journals Incommensurately Modulated Crystal Structure and Photoluminescence Properties of Eu2O3- and P2O5-Doped Ca2SiO4 Phosphor

Materials ◽  
2019 ◽  
Vol 13 (1) ◽  
pp. 58
Author(s):  
Hiromi Nakano ◽  
Shota Ando ◽  
Konatsu Kamimoto ◽  
Yuya Hiramatsu ◽  
Yuichi Michiue ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Light Emission ◽  
Red Light ◽  
Basic Unit ◽  
Β Phase ◽  
Stacking Order ◽  
Cell Dimensions ◽  
Incommensurate Modulation ◽  
Unit Cell Dimensions ◽  
Identical Chemical Composition

We prepared four types of Eu2O3- and P2O5-doped Ca2SiO4 phosphors with different phase compositions but identical chemical composition, the chemical formula of which was (Ca1.950Eu3+0.013☐0.037)(Si0.940P0.060)O4 (☐ denotes vacancies in Ca sites). One of the phosphors was composed exclusively of the incommensurate (IC) phase with superspace group Pnma(0β0)00s and basic unit-cell dimensions of a = 0.68004(2) nm, b = 0.54481(2) nm, and c = 0.93956(3) nm (Z = 4). The crystal structure was made up of four types of β-Ca2SiO4-related layers with an interlayer. The incommensurate modulation with wavelength of 4.110 × b was induced by the long-range stacking order of these layers. When increasing the relative amount of the IC-phase with respect to the coexisting β-phase, the red light emission intensity, under excitation at 394 nm, steadily decreased to reach the minimum, at which the specimen was composed exclusively of the IC-phase. The coordination environments of Eu3+ ion in the crystal structures of β- and IC-phases might be closely related to the photoluminescence intensities of the phosphors.

scholarly journals The crystal and molecular structure of the bis(N,N,N′,N′-tetramethylethanediamine) adduct of I(Br)InInBr2, In2Br3I•2C6H16N2, an indium–indium bonded molecule

1984 ◽  
Vol 62 (3) ◽  
pp. 601-605 ◽  
Author(s):  
Masood A. Khan ◽  
Clovis Peppe ◽  
Dennis G. Tuck
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Crystal And Molecular Structure ◽  
Heavy Atom ◽  
Orthorhombic Space Group ◽  
Trigonal Bipyramidal ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Heavy Atom Method ◽  
Distorted Trigonal Bipyramidal

The crystal structure of the title compound has been determined by the heavy atom method. The crystals are orthorhombic, space group Pbca, with unit cell dimensions a = 22.795(3) Å, b = 17.518(2) Å, c = 12.396(3) Å, Z = 8; R = 0.0409 for 1527 unique "observed" reflections. The structure is disordered, with each halogen site (X) occupied by 75% Br, 25% I. The molecule consists of two X2(tmen)In units (tmen = N,N,N′,N′-tetramethylethanediamine) with distorted trigonal bipyramidal geometry, joined by an In—In bond 2.775(2) Å in length.

Structural Studies on N-(2,4,6-Trimethylphenyl)-methyl/ chloro-acetamides, 2,4,6-(CH3)3C6H2NH-CO-CH3–yXy (X = CH3 or Cl and y = 0, 1, 2)

2006 ◽  
Vol 61 (10-11) ◽  
pp. 588-594 ◽  
Author(s):  
Basavalinganadoddy Thimme Gowda ◽  
Jozef Kožíšek ◽  
Hartmut Fuess
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structural Data ◽  
The Other ◽  
Side Chain ◽  
Structural Studies ◽  
Asymmetric Unit ◽  
Lattice Constants ◽  
Peptide Linkage ◽  
The Mean

TMPAThe effect of substitutions in the ring and in the side chain on the crystal structure of N- (2,4,6-trimethylphenyl)-methyl/chloro-acetamides of the configuration 2,4,6-(CH3)3C6H2NH-COCH3− yXy (X = CH3 or Cl and y = 0,1, 2) has been studied by determining the crystal structures of N-(2,4,6-trimethylphenyl)-acetamide, 2,4,6-(CH3)3C6H2NH-CO-CH3 (); N-(2,4,6- trimethylphenyl)-2-methylacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH2-CH3 (TMPMA); N-(2,4,6- trimethylphenyl)-2,2-dimethylacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH(CH3)2 (TMPDMA) and N-(2,4,6-trimethylphenyl)-2,2-dichloroacetamide, 2,4,6-(CH3)3C6H2NH-CO-CHCl2 (TMPDCA). The crystallographic system, space group, formula units and lattice constants in Å are: TMPA: monoclinic, Pn, Z = 2, a = 8.142(3), b = 8.469(3), c = 8.223(3), β = 113.61(2)◦; TMPMA: monoclinic, P21/n, Z = 8, a = 9.103(1), b = 15.812(2), c = 16.4787(19), α = 89.974(10)◦, β = 96.951(10)◦, γ =89.967(10)◦; TMPDMA: monoclinic, P21/c, Z = 4, a =4.757(1), b= 24.644(4), c =10.785(2), β = 99.647(17)◦; TMPDCA: triclinic, P¯1, Z = 2, a = 4.652(1), b = 11.006(1), c = 12.369(1), α = 82.521(7)◦, β = 83.09(1)◦, γ = 79.84(1)◦. The results are analyzed along with the structural data of N-phenylacetamide, C6H5NH-CO-CH3; N-(2,4,6-trimethylphenyl)-2-chloroacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH2Cl; N-(2,4,6-trichlorophenyl)-acetamide, 2,4,6-Cl3C6H2NH-COCH3; N-(2,4,6-trichlorophenyl)-2-chloroacetamide, 2,4,6-Cl3C6H2NH-CO-CH2Cl; N-(2,4,6-trichlorophenyl)- 2,2-dichloroacetamide, 2,4,6-Cl3C6H2NH-CO-CHCl2 and N-(2,4,6-trichlorophenyl)- 2,2,2-trichloroacetamide, 2,4,6-Cl3C6H2NH-CO-CCl3. TMPA, TMPMA and TMPDCA have one molecule each in their asymmetric units, while TMPDMA has two molecules in its asymmetric unit. Changes in the mean ring distances are smaller on substitution as the effect has to be transmitted through the peptide linkage. The comparison of the other bond parameters reveal that there are significant changes in them on substitution.

scholarly journals X-ray Crystallographic Study of Ranaconitine

2011 ◽  
Vol 6 (11) ◽  
pp. 1934578X1100601
Author(s):  
Yang Li ◽  
Jun-Hui Zhou ◽  
Gui-Jun Han ◽  
Min-Juan Wang ◽  
Wen-Ji Sun ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Diffraction Analysis ◽  
Critical Role ◽  
X Ray Diffraction ◽  
Monoclinic System ◽  
X Ray ◽  
Crystallographic Study ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

The crystal structure of natural diterpenoid alkaloid ranaconitine isolated from Aconitum sinomontanum Nakai has been determined by single crystal X-ray diffraction analysis. The crystal presents a monoclinic system, space group C2 with Z = 4, unit cell dimensions a = 30.972(19) Å, b = 7.688(5) Å, and c = 19.632(12) Å. Moreover, the intermolecular O–H···O hydrogen bonds and weak π-π interactions play a critical role in expanding the dimensionality.

Preliminary crystallographic studies on glutamine synthetase from Mycobacterium tuberculosis

1999 ◽  
Vol 55 (4) ◽  
pp. 865-868 ◽  
Author(s):  
Harindarpal S. Gill ◽  
Gaston M.U. Pfluegl ◽  
David Eisenberg
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Glutamine Synthetase ◽  
Etiologic Agent ◽  
Asymmetric Unit ◽  
Crystal Forms ◽  
X Ray ◽  
Cell Dimensions ◽  
The One ◽  
Unit Cell Dimensions ◽  
Axes Of Symmetry

The etiologic agent of tuberculosis, Mycobacterium tuberculosis, has been shown to secrete the enzyme glutamine synthetase (TB-GS) which is apparently essential for infection. Four crystal forms of a recombinant TB-GS were grown. The one chosen for synchrotron X-ray data collection belongs to space group P212121 with unit-cell dimensions 208 × 258 × 274 Å, yielding 2.4 Å resolution data. A Matthews number of 2.89 Å3 Da−1 is found, corresponding to 24 subunits of molecular mass 1300 kDa in the asymmetric unit. From earlier work, the structure of Salmonella typhimurium GS, which is 51% identical in sequence to TB-GS, is known to be dodecameric with 622 symmetry. Self-rotation calculations on the TB-GS X-ray data reveal only one set of sixfold and twofold axes of symmetry. A Patterson map calculated from the native X-ray data confirms that there are two dodecamers in the asymmetric unit, having both their sixfold and twofold axes parallel to one another.

Crystallization and preliminary diffraction analysis of the HincII restriction endonuclease–DNA complex

1999 ◽  
Vol 55 (11) ◽  
pp. 1943-1945 ◽  
Author(s):  
Nancy C. Horton ◽  
Lydia F. Dorner ◽  
Ira Schildkraut ◽  
John J. Perona
Keyword(s):  
High Energy ◽  
Asymmetric Unit ◽  
Hanging Drop ◽  
Data Set ◽  
Synchrotron Source ◽  
Polyethylene Glycol 4000 ◽  
Dimeric Complexes ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Dna Complex

Crystals of the 60 kDa dimeric HincII restriction enzyme bound to a 12 base-pair dyad-symmetric duplex DNA carrying the specific 5′-GTCGAC recognition site have been obtained. Crystals grew by hanging-drop vapor diffusion from solutions containing polyethylene glycol 4000 as precipitating agent. The rod-shaped crystals belong to space group I222 (or I212121), with unit-cell dimensions a = 66.9, b = 176.7, c = 256.0 Å. There are most likely to be two dimeric complexes in the asymmetric unit. A complete native data set has been collected from a high-energy synchrotron source to a resolution of 2.5 Å at 100 K, with an R merge of 4.8%.

scholarly journals The reaction of 3,5-diphenyl-1,2-dithiolium-4-olate with aniline: the crystal structure of 1-phenylimino-2-phenylamino-3-phenylindene

1987 ◽  
Vol 65 (12) ◽  
pp. 2830-2833 ◽  
Author(s):  
David M. McKinnon ◽  
Peter D. Clark ◽  
Robert O. Martin ◽  
Louis T. J. Delbaere ◽  
J. Wilson Quail
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Single Crystal ◽  
Least Squares ◽  
Direct Methods ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

3,5-Diphenyl-1,2-dithiolium-4-olate (1) reacts with aniline to form 1-phenylimino-2-phenylamino-3-phenylindene (3a). Under suitable conditions, 6-phenylbenzo[b]indeno[1,2-e]-1,2-thiazine is also formed. These structures are confirmed by alternative syntheses. The molecular structure of 3a has been determined by single crystal X-ray diffraction. Compound 3a crystallizes in the monoclinic space group C2/c with unit cell dimensions a = 20.777(3) Å, b = 6.130(3) Å, c = 31.327(3) Å, 3 = 99.59(1)°, and Z = 8. The structure was solved by direct methods and refined by least squares to a final R = 0.055. The molecular structure of 3a shows the three phenyl containing substituents to have the planes of their ring systems tilted between 40° and 60° from the plane of the indene system due to steric repulsions.

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