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PDB ID Mentions in PubMed Central Article count: 1

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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

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 B... SSY 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.

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.

Crystal data * Tgt(Cys158Val) Tgt(Cys158Val)·guanine Tgt(Cys158Val)·preQ 1 Tgt(Cys158Val)·queuine PDB ID 4gd0 4h7z 4e2v 4hvx A. Data Collection and Processing Beamline BL 14.2 BL 14.1 BL 14.2 BL 14.2 λ (Å) 0.91841 0.91841 0.91841 0.91841 Space group C 2 C2 C 2 C 2 a , b , c (Å) 91.4, 65.0, 70.2 90.4, 64,8, 70,8 90.4, 64.9, 70.4 91.6, 64.5, 71.1 β (°) 96.1 95.6 95.8 96.2 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) 50-1.29 (1.31-1.29) 30-1.68 (1.77-1.68) 21-1.18 (1.2-1.18) 50-1.82 (1.85-1.82) No.

Data processing and scaling was performed using the HKL2000 package [50] except for structure 4h7z which was processed using iMOSFLM 1.0.6 [51] and SCALA [52] .

For the structures 4h7z , 4hvx , 4hqv , 4hsh an additional optimization of the weights between X-ray target and stereochemistry as well as between ADP restraints was performed by PHENIX 1.8-1069 [55] .

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] .

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.

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] .

Publication Year: 2013