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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
vapour-diffusion with sitting drops, structure of a truncated enzyme form (residues 71-679 with a C-terminal His tag), structure of a truncated enzyme form (residues 71-679 with a C-terminal His tag) complexed with GTP, determined at 2.9 A resolution
in complex with its protein primer VPg and diphosphate, hanging drop vapour diffusion method, in 20 mM Tris (pH 9.0), 300 mM NaCl, 15% glycerol, 0.5 mM Tris(2-carboxyethyl)phosphine
hanging-drop vapor diffusion method at 4°C, three-dimensional structure of a catalytically active DENV RdRp domain determined to 1.85 A resolution by X-ray crystallography
native and in complex with inhibitor 5-[[(4-chlorophenyl)sulfonyl]amino]-2-methyl-1-benzofuran-3-carboxylic acid, to 1.79 and 2.1 A resolution, respectively. The inhibitor binds to the protein as a dimer and causes conformational changes in the protein
purified enzyme in complex with NTP substrate, X-ray diffraction structure determination and analysis at 2.45-2.78 A resolution, analysis of multiple nucleotide-incorporation events and different NAC states
hanging drop vapor diffusion at 16°C using 12 mg/ml protein. Full-length enzyme at 2.0 A resolution, enzyme in complex with GTP at 2.35 A resolution, mutant enzyme G1A and and DELTA68
structure of Qbeta replicase complex, to 2.5 A resolution. Qbeta replicase is composed of the bacteriophage Qbeta catalytic beta-subunit as well as the Escherichia coli host translation elongation factors EF-Tu and EF-Ts. The basic catalytic machinery in the viral subunit appears similar to other RNA-dependent RNA polymerases, while a C-terminal region of the beta-subunit engages in extensive interactions with EF-Tu and may contribute to the separation of the transient duplex formed between the template and the nascent product to allow exponential amplification of the phage genome
hanging-drop vapour-diffusion method, structure of the enzyme in a free form at 1.9 A resolution and in complex with a template-primer RNA decanucleotide at 3.0 A resolution
HCV NS5B polymerase by hanging drop method at room temperature using a well buffer of 20% PEG 4000, 50 mM ammonium sulfate, 100 mM sodium acetate, pH 4.7, with 5 mM DTT, complexes are prepared by soaking the crystals for 3-24 h in solutions containing 15-20% DMSO, 20% glycerol, 20% PEG 4000, 0.1 M Hepes and 10 mM MgCl2 at pH 7.6 and an inhibitor concentration of 2-10 mM, X-ray diffraction structure determination and analysis at 2.6 A resolution for compound 29 and 2.15 A for compound 49
a large fragment of subunit PA bound to a fragment of subunit PB1, hanging dropn vapour diffusion method, 20°C, mixing of 0.001 ml of protein solution, containing 10 mg/ml protein in 20 mM Tris-HCl, pH 8.0, and 100 mM sodium chloride, and 0.001 ml of reservoir solution consisting of 100 mM Tris-HCl, pH 7.5, and 2.4 M sodium formate, X-ray diffraction structure determination and analysis at 2.3 A resolution
purified recombinant enzyme, at 20°C by the hanging drop method using a protein solution of 5-10 mg/ml protein in 20 mM Tris-HCl, pH 8.0, 100 mM NaCl and 2.5 mM MnCl2 and a reservoir composition of 1.2 M Li2SO4, 100 mM MES, pH 6.0, 10 mM Mg acetate and 3% ethylene glycol
purified apo-FluPol in closed conformation, sitting-drop vapour-diffusion, protein:precipitant ratio of 2:1, mixing of 5 mg/ml protein with either 70% v/v Morpheus G2, supplemented with 0%-1% 1 M NaOH, to generate P43212 crystals, or with crystal-seeds and 0.2 M NaCl, 0.1 M Na-HEPES, pH 7.5, and 25% w/v PEG 4000 for P212121 crystals, 20°C, heavy atom derivatization by P43212 crystals soaking in a solution of gold(I) potassium cyanide dissolved in mother liquor, for 2-3 h at 20°C, X-ray diffraction structure determination and analysis at 3.9 A resolution
purified recombinant enzyme in apo-form or in complex with ATP or GTP, jRdRp (0.08 mM) is incubated with GTP/ATP (5 mM) for 30 min before setting crystallization trials, screening and method optimization, hanging drop vapour diffusion method, mixing of protein-ATP/GTP with 10-18% w/v PEG 4000, 100 mM Tris-Cl buffer, pH 8.0, and 7% v/v 1-propanol, 25°C, for the apo-enzyme mixing of 0.096 mM protein with 10-15% PEG 5000 mono methyl ether, 100 mM Tris-Cl, pH 8.0, and 200mM NaSCN, 25°C, X-ray diffraction structure determination and analysis at 2.28-3.65 A resolution, molecular replacement using the apo-enzyme structures of WNV and DENV, PDB IDs 2HFZ and 2J7W, as search models
in-silico docking search of inhibitors. The location of inhibitors 8,8'-[carbonylbis(iminobenzene-3,1-diylcarbonylimino)]dinaphthalene-1,3,5-trisulfonic acid and Suramin inner head is stabilized by offset-tilted aromatic/aromatic interaction with residue Trp42
in-silico docking search of inhibitors. The location of inhibitors 8,8'-[carbonylbis(iminobenzene-3,1-diylcarbonylimino)]dinaphthalene-1,3,5-trisulfonic acid and Suramin inner head is stabilized by offset-tilted aromatic/aromatic interaction with residue Trp41
a complex of Norovirus RNA-dependent RNA polymerase bound to Mn2+ and an RNA primer-template duplex is investigated using X-ray crystallography and hybrid quantum chemical/molecular mechanical simulations. The complex crystallizes in a tetragonal crystal form. The nature of the primer/template duplex binding in the resulting structure indicates that the complex is a closed back-tracked state of the enzyme, in which the 3'-end of the primer occupies the position expected for the postincorporated nucleotide before translocation. Computationally, it is found that the complex can accept a range of divalent metal cations without marked distortions in the active site structure. The highest binding energy is for copper, followed closely by manganese and iron, and then by zinc, nickel, and cobalt
enzyme in two crystal forms A and B, method screening, 300 nl of 6-20 mg/ml protein in 50 mM Tris, 100 mM NaCl, and 2 mM DTT, pH 8.0, are mixed with reservoir solution containing 4.0 M sodium formate, 0.2 M magnesium formate, and 20% w/v PEG 3350, in hanging drops at 20°C, or with 4.3 M NaCl, 0.1 M HEPES, and 30 mM tri-glycine in sitting drops at room temperature, X-ray diffraction structure determination and analysis at resolutions of 1.7 A and 2.1 A, respectively. Form A contains Mg2+ bound at a site that deviates from the canonical non-catalytic position seen in form B
structure of Qbeta replicase complex, to 2.5 A resolution. Qbeta replicase is composed of the bacteriophage Qbeta catalytic beta-subunit as well as the Escherichia coli host translation elongation factors EF-Tu and EF-Ts. The basic catalytic machinery in the viral subunit appears similar to other RNA-dependent RNA polymerases, while a C-terminal region of the beta-subunit engages in extensive interactions with EF-Tu and may contribute to the separation of the transient duplex formed between the template and the nascent product to allow exponential amplification of the phage genome