scholarly journals Characterisation and structure determination of a llama-derived nanobody targeting the J-base binding protein 1

2018 ◽  
Author(s):  
Bart Van Beusekom ◽  
Tatjana Heidebrecht ◽  
Athanassios Adamopoulos ◽  
Alexander Fish ◽  
Els Pardon ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Protein ◽  
The Other ◽  
Free State ◽  
Asymmetric Unit ◽  
Single Domain Antibody ◽  
High Affinity ◽  
Domain Antibody ◽  
Ligand Free ◽  
Complementarity Determining Regions

AbstractThe J-base Binding Protein 1 (JBP1) contributes to biosynthesis and maintenance of base J (β-D-glucosyl-hydroxymethyluracil), a modification of thymidine confined to some protozoa. Camelid (llama) single domain antibody fragments (nanobodies) targeting JBP1 were produced for use as crystallization chaperones. Surface plasmon resonance (SPR) screening identified Nb6 as a strong binder, recognising JBP1 with a 1:1 stoichiometry and high affinity (kD=30nM). Crystallisation trials of JBP1 in complex with Nb6, yielded crystals diffracting to 1.47Å resolution.However, the asymmetric unit dimensions and molecular replacement with a nanobody structure, clearly showed that the crystals of the expected complex with JBP1 were of the nanobody alone. Nb6 crystallizes in spacegroup P31 with two molecules in the asymmetric unit; its crystal structure was refined to a final resolution of 1.64Å. Ensemble refinement suggests that on the ligand-free state one of the complementarity determining regions (CDRs) is flexible while the other two adopt well-defined conformations.SynopsisA camelid single domain antibody fragment (nanobody) is shown to have high affinity towards its recognition target, the J-base binding protein 1 (JBP1). The serendipitous crystallisation of this nanobody alone, and its crystal structure solution and refinement to 1.64Å resolution are described. Ensemble refinement suggests that on the ligand-free state one of the complementarity determining regions (CDRs) is flexible while the other two adopt well-defined conformations.

scholarly journals Characterization and structure determination of a llama-derived nanobody targeting the J-base binding protein 1

2018 ◽  
Vol 74 (11) ◽  
pp. 690-695 ◽  
Author(s):  
Bart van Beusekom ◽  
Tatjana Heidebrecht ◽  
Athanassios Adamopoulos ◽  
Alexander Fish ◽  
Els Pardon ◽  
...  
Keyword(s):  
Binding Protein ◽  
Antibody Fragments ◽  
Molecular Replacement ◽  
Asymmetric Unit ◽  
Single Domain Antibody ◽  
High Affinity ◽  
Domain Antibody ◽  
Ligand Free ◽  
Complementarity Determining Regions

J-base binding protein 1 (JBP1) contributes to the biosynthesis and maintenance of base J (β-D-glucosylhydroxymethyluracil), a modification of thymidine confined to some protozoa. Camelid (llama) single-domain antibody fragments (nanobodies) targeting JBP1 were produced for use as crystallization chaperones. Surface plasmon resonance screening identified Nb6 as a strong binder, recognizing JBP1 with a 1:1 stoichiometry and high affinity (K d = 30 nM). Crystallization trials of JBP1 in complex with Nb6 yielded crystals that diffracted to 1.47 Å resolution. However, the dimensions of the asymmetric unit and molecular replacement with a nanobody structure clearly showed that the crystals of the expected complex with JBP1 were of the nanobody alone. Nb6 crystallizes in space group P31 with two molecules in the asymmetric unit; its crystal structure was refined to a final resolution of 1.64 Å. Ensemble refinement suggests that in the ligand-free state one of the complementarity-determining regions (CDRs) is flexible, while the other two adopt well defined conformations.

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 Synthesis and crystal structure of (E)-1,2-bis[2-(methylsulfanyl)phenyl]diazene

2019 ◽  
Vol 75 (11) ◽  
pp. 1808-1811
Author(s):  
Jonas Hoffmann ◽  
Thomas J. Kuczmera ◽  
Enno Lork ◽  
Anne Staubitz
Keyword(s):  
Crystal Structure ◽  
Dimethyl Disulfide ◽  
Hirshfeld Surface ◽  
The Other ◽  
Inversion Symmetry ◽  
Asymmetric Unit ◽  
Synthesis And Crystal Structure ◽  
Compound C ◽  
Azo Group ◽  
Subsequent Quenching

The title compound, C14H14N2S2, was obtained by transmetallation of 2,2′-bis(trimethylstannyl)azobenzene with methyl lithium, and subsequent quenching with dimethyl disulfide. The asymmetric unit comprises two half-molecules, the other halves being completed by inversion symmetry at the midpoint of the azo group. The two molecules show only slight differences with respect to N=N, S—N and aromatic C=C bonds or angles. Hirshfeld surface analysis reveals that except for one weak H...S interaction, intermolecular interactions are dominated by van der Waals forces only.

scholarly journals Crystal structure of the co-crystalline adduct 1,3,6,8-tetraazatricyclo[4.4.1.13,8]dodecane (TATD)–4-bromophenol (1/2)

2015 ◽  
Vol 71 (5) ◽  
pp. 463-465 ◽  
Author(s):  
Augusto Rivera ◽  
Juan Manuel Uribe ◽  
Jicli José Rojas ◽  
Jaime Ríos-Motta ◽  
Michael Bolte
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Rotation Axis ◽  
The Other ◽  
Two Dimensional ◽  
Asymmetric Unit ◽  
Species Association ◽  
Crystalline Adduct ◽  
Aminal Cage

The structure of the 1:2 co-crystalline adduct C8H16N4·2C6H5BrO, (I), from the solid-state reaction of 1,3,6,8-tetraazatricyclo[4.4.1.13,8]dodecane (TATD) and 4-bromophenol, has been determined. The asymmetric unit of the title co-crystalline adduct comprises a half molecule of aminal cage polyamine plus a 4-bromophenol molecule. A twofold rotation axis generates the other half of the adduct. The primary inter-species association in the title compound is through two intermolecular O—H...N hydrogen bonds. In the crystal, the adducts are linked by weak non-conventional C—H...O and C—H...Br hydrogen bonds, giving a two-dimensional supramolecular structure parallel to thebcplane.

scholarly journals Crystal structure of 1,3-bis(4-hexyl-5-iodothiophen-2-yl)-4,5,6,7-tetrahydro-2-benzothiophene

2014 ◽  
Vol 70 (10) ◽  
pp. o1133-o1134
Author(s):  
Julian Linshoeft ◽  
Christian Näther ◽  
Anne Staubitz
Keyword(s):  
Crystal Structure ◽  
Title Compound ◽  
The Other ◽  
Dihedral Angles ◽  
Asymmetric Unit ◽  
Compound C ◽  
Independent Molecules

In the crystal structure of the title compound, C28H36I2S3, a terthiophene monomer, the central thiophene unit is arrangedanti-coplanar to the two outer thiophene rings. There are two crystallographically independent molecules in the asymmetric unit, which show different conformations. In one molecule, the dihedral angles between the inner and the two outer thiophene rings are 15.7 (3) and 3.47 (3)°, whereas these values are 4.2 (3) and 11.3 (3)° for the second molecule. Differences are also found in the arrangement of the hexyl chains: in one of the two molecules, both chains are nearly in plane to the central moiety, whereas in the second molecule, only one chain is in plane and the other one is nearly perpendicular to the central moiety. Some of the C atoms are disordered and were refined using a split model with occupancy ratios of 0.65:0.35 and 0.70:0.30 in the two molecules.

scholarly journals Competitive Selection from Single Domain Antibody Libraries Allows Isolation of High-Affinity Antihapten Antibodies That Are Not Favored in the llama Immune Response

2011 ◽  
Vol 83 (18) ◽  
pp. 7213-7220 ◽  
Author(s):  
Sofia Tabares-da Rosa ◽  
Martin Rossotti ◽  
Carmen Carleiza ◽  
Federico Carrión ◽  
Otto Pritsch ◽  
...  
Keyword(s):  
Immune Response ◽  
Single Domain ◽  
Single Domain Antibody ◽  
Competitive Selection ◽  
High Affinity ◽  
Domain Antibody ◽  
Antibody Libraries

[5,10,15,20-Tetrakis(2,6-dimethoxyphenyl)porphyrinato]nickel(II)–toluene–dichloromethane (3/2/4):a mixed solvate

2007 ◽  
Vol 63 (11) ◽  
pp. m2824-m2824
Author(s):  
Diane Conrad ◽  
Jennifer DeCoskey ◽  
Christopher Yeisley ◽  
Matthias Zeller ◽  
Allen D. Hunter ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Glacial Acetic Acid ◽  
Electronic Spectroscopy ◽  
The Other ◽  
Inversion Center ◽  
Asymmetric Unit ◽  
Nickel Ion ◽  
H Nmr ◽  
Nmr Data ◽  
Toluene Molecule

The crystal structure, electronic spectroscopy, and 1H NMR data for the title compound, [Ni(C52H44N4O8)]·0.67C7H8·1.33CH2Cl2, are reported. The compound was prepared by the reaction of nickel(II) acetate with the ligand in refluxing glacial acetic acid. The asymmetric unit consists of 1.5 nickel porphyrins, two dichloromethane molecules and one toluene molecule. One of the nickel–porphyrinate molecules is located on an inversion center and is planar in the solid state, while the other assumes a saddle-shaped geometry. In both cases, the nickel ion is four-coordinate.

scholarly journals Crystal structure ofN-carbamothioyl-2-methylbenzamide

2015 ◽  
Vol 71 (6) ◽  
pp. o425-o425 ◽  
Author(s):  
Farook Adam ◽  
Nadiah Ameram ◽  
Wai Mun Tan
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Aromatic Ring ◽  
Dihedral Angle ◽  
Title Compound ◽  
The Other ◽  
Asymmetric Unit ◽  
Compound C

There are two molecules in the asymmetric unit of the title compound, C9H10N2OS. In one, the dihedral angle between the aromatic ring and the carbamothioyl group is 52.31 (7)° and in the other it is 36.16 (6)°. Each molecule features an intramolecular N—H...O hydrogen bond, which generates anS(6) ring and the O and S atoms have anantidisposition. In the crystal, molecules are linked by N—H...S and N—H...O hydrogen bonds, generating separate [130] and [1-30] infinite chains. Weak C—H...O and C—H...S interactions are also observed.

scholarly journals Crystal structure of ammonium 3′-azido-3′-deoxythymidine-5′-aminocarbonylphosphonate hemihydrate: an anti-HIV agent

2014 ◽  
Vol 70 (11) ◽  
pp. 396-399
Author(s):  
Maxim V. Jasko ◽  
Galina V. Gurskaya ◽  
Marina K. Kukhanova ◽  
Ivan S. Bushmarinov
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Rotation Axis ◽  
Three Dimensional ◽  
Amide Group ◽  
The Other ◽  
Asymmetric Unit ◽  
Anti Hiv

The asymmetric unit of the title compound, NH4+·C11H14N6O7P−·0.5H2O, contains one 3′-azido-3′-deoxythymidine-5′aminocarbonylphosphonate (ACP–AZT) anion, half of an NH4+cation lying on a twofold rotation axis and in another position, occupied with equal probabilities of 0.5, an NH4+cation and a water molecule. The amide group of the ACP–AZT anion is disordered (occupancy ratio 0.5:0.5), with one part forming an N—H...O (involving C=O...H4N+) hydrogen bond and the other an O—H...N (involving C—NH2...OH2) hydrogen bond with the components of the split NH4+/H2O position. The pseudorotation parameters of ACP–AZT set it apart from previously studied AZT and thymidine. In the crystal, the various components are linked by N—H...O, O—H...O, N—H...N, C—H...O and C—H...N hydrogen bonds, forming a three-dimensional framework.

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