Primary Citation PubMed: 23704982
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
Data mentions are occurrences of PDB IDs in the full text articles from the
PubMedCentral Open Access Subset
of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed.
Article titles can be filtered by keywords and sorted by year.
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.
Crystal data * Tgt(Cys158Val/Val233Gly) Tgt(Cys158Val/Val233Gly)·preQ 1 Tgt(Cys158Val/Val233Gly)·queuine “WT”-Tgt·queuine PDB ID 4h6e 4gcx 4hqv ** A. Data Collection 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  with 5% to 10% of all data being used for R free calculation and followed by repeated cycles of maximum likehood energy minimization.
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  .
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  .
Publication Year: 2013
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.