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Primary Citation PubMed: 23704982 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 1

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PDB ID Mentions in PubMed Central

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Investigation of specificity determinants in bacterial tRNA-guanine transglycosylase reveals queuine, the substrate of its eucaryotic counterpart, as inhibitor.

(2013) PLoS One 8

PubMed: 23704982 | PubMedCentral: PMC3660597 | DOI: 10.1371/journal.pone.0064240

Crystal data * Tgt(Cys158Val/Val233Gly) Tgt(Cys158Val/Val233Gly)·preQ 1 Tgt(Cys158Val/Val233Gly)·queuine “WT”-Tgt·queuine PDB ID 4h6e 4gcx 4hqv ** A. Data Colle... tion and Processing Beamline BL 14.2 BL 14.2 BL 14.2 BL 14.2 λ (Å) 0.91841 0.91841 0.91841 0.91841 Space group C2 C2 C2 C2 a , b , c (Å) 91.0, 64.8, 70.5 91.2, 65.1, 70.6 90.9, 65.0, 70.6 90.8, 64.7, 70.6 β (°) 96.1 96.1 96.3 95.9 Matthews coefficient (Å 3 /Da) 2.4 2.4 2.4 2.4 Solvent content (%) 48.7 48.7 48.7 48.7 B Diffraction Data Resolution range a (Å) 30-1.42 (1.44-1.42) 50-1.42 (1.44-1.42) 50-1.66 (1.69-1.66) 50-1.22(1.24-1.22) No.

For the structures 4e2v , 4dg0 , 4h7z , 4h6e , 4hqv , 4hsh , 4hqv , 4gcx and “WT”-Tgt·queuine refinement was performed with PHENIX 1.8-1069 [55] with 5% to 10% of all data being used for R free calculation and followed by repeated cycles of maximum likehood energy minimization.

The temperature factors (individual B -factors) for structures 4e2v , 4gcx , 4gd0 and 3bld were anisotropically refined, whereas for structures 4hvx , 4h7z , 4hsh , 4hqv and 4h6e and “WT”-Tgt·queuine TLS refinement was applied.

For structures 4e2v , 4dg0 , 4h7z , 4h6e , 4hqv , 4hsh , 4hqv , 4gcx and “WT”-Tgt·queuine water was located using the refinement settings “update waters” implemented in the program PHENIX 1.8-1068 [55] .

Coordinates of the apo-Tgt crystal structure (PDB-code: 1pud in case of the structures 3bl3 , 3bld , 3blo ) or rather coordinates of Tgt in complex with 2-[(thiophen-2-ylmethyl)amino]-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one (PDB-code: 3gev in case of structures 4dg0 , 4e2v , 4hvx , 4h7z , 4h6e , 4hsh , 4hqv , 4gcx and “WT”-Tgt·queuine) were slightly modified (deletion of water and ligand as well as coordinates at the sites of mutation) before applying for initial rigid-body refinement of the protein molecule followed by repeated cycles of conjugate gradient energy minimisation, simulated annealing and B -factor refinement using the CNS program package [53] .

Data sets ( 3bld , 4dg0 , 4e2v , 4hvx , 4h7z , 4h6e , 4hsh , 4hqv , 4gcx and “WT”-Tgt·queuine) were collected at cryo conditions (−173°C≡100 K) at the BESSY II (Helmholz-Zentrum, Berlin, Germany) beamlines BL-14.1 (λ = 0.91841 Å) and BL-14.2 (λ = 0.91841 Å) and with CuKα radiation (λ = 1.5418 Å) using a Rigaku RU-300 rotating-anode generator at 50 kV and 90 mA equipped with Xenocs focussing optics and an R-AXIS IV detector.

Publication Year: 2013