Primary Citation PubMed: 23704982
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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
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-i... idazo[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  .
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.
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.
Refinement at the later stages was performed with SHELXL  for structures 3bl3 , 3bld , and 3blo .
Crystal data * Tgt(Val233Gly) Tgt(Val233Gly)·preQ 1 Tgt(Val233Gly)·queuine PDB ID 3bl3 3bld 4hsh A. Data Collection and Processing Beamline In-house BL 14.2 BL 14.2 λ (Å) 1.54178 0.91841 0.91841 Space group C 2 C 2 C 2 a , b , c (Å) 90.7, 64.8, 70.4 89.7, 64.9, 70.3 90.5, 64.8, 70.5 β (°) 95.9 95.6 95.9 Matthews coefficient (Å 3 /Da) 2.4 2.4 2.4 Solvent content (%) 48.7 48.7 48.7 B. Diffraction Data Resolution range a (Å) 50-2.25 (2.30-2.25) 50-1.19 (1.22 -1.19) 50-1.56 (1.59-1.56) No.
Publication Year: 2013
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