Retraction of Mechanistic Basis for Epstein–Barr Virus Ribonucleotide-reductase Small-Subunit Function

Retraction of Mechanistic Basis for Epstein–Barr Virus Ribonucleotide-reductase Small-Subunit Functio

DSF melting curves of TS_VZV with BVDU_P.

<p>(a) BVDU could not stabilize TS_VZV before phosphorylation but after an <i>in vitro</i> phosphorylation with TK_HS, BVDU_P increased the T_m of TS_VZV by a larger extent than dUMP. (b) Varying concentrations of BVDU_P increased the T_m of TS_VZV in a dose responsive manner. (c) Further stabilization of TS_VZV was observed in the presence of 100 μM raltitrexed with 100 μM of BVDU_P.</p

Data collection and refinement statistics on the apo and complex structures of TS_VZV.

<p>^a The values in the parentheses are for the highest resolution shell (3.1–3.2 Å).</p><p>^b The values in the parentheses are for the highest resolution shell (2.9–3.0 Å).</p><p>^c<math><mrow><msub><mi>R</mi><mrow><mi>m</mi><mi>e</mi><mi>r</mi><mi>g</mi><mi>e</mi></mrow></msub><mo>=</mo><mrow><mrow><mo>[</mo><mrow><msub><mo>∑</mo><mrow><mi>h</mi><mi>k</mi><mi>l</mi></mrow></msub><msub><mo>∑</mo><mi>i</mi></msub><mrow><mo>|</mo><mrow><msub><mi>I</mi><mi>i</mi></msub><mrow><mo>(</mo><mrow><mi>h</mi><mi>k</mi><mi>l</mi></mrow><mo>)</mo></mrow><mo>−</mo><mi>I</mi><mo>¯</mo><mrow><mo>(</mo><mrow><mi>h</mi><mi>k</mi><mi>l</mi></mrow><mo>)</mo></mrow></mrow><mo>|</mo></mrow></mrow><mo>]</mo></mrow></mrow><mrow><mrow><mo>[</mo><mrow><msub><mo>∑</mo><mrow><mi>h</mi><mi>k</mi><mi>l</mi></mrow></msub><msub><mo>∑</mo><mi>i</mi></msub><mi>I</mi><mo>¯</mo><mrow><mo>(</mo><mrow><mi>h</mi><mi>k</mi><mi>l</mi></mrow><mo>)</mo></mrow></mrow><mo>]</mo></mrow></mrow><mo>×</mo><mn>100</mn></mrow></math>, where <i>I</i>_<i>i</i> is the <i>i</i>th intensity measurement of reflection <i>hkl</i>, <i>Ī(hkl)</i> is the mean intensity measurement of the symmetry related or replicated reflections of the unique reflection <i>hkl</i>.</p><p>^d<math><mrow><msub><mi>R</mi><mrow><mi>f</mi><mi>a</mi><mi>c</mi><mi>t</mi><mi>o</mi><mi>r</mi></mrow></msub><mo>=</mo><mrow><mrow><mo>[</mo><mrow><msub><mo>∑</mo><mrow><mi>h</mi><mi>k</mi><mi>l</mi></mrow></msub><mrow><mo>|</mo><mrow><msub><mi>F</mi><mrow><mi>o</mi><mi>b</mi><mi>s</mi></mrow></msub><mrow><mo>(</mo><mrow><mi>h</mi><mi>k</mi><mi>l</mi></mrow><mo>)</mo></mrow><mo>−</mo><msub><mi>F</mi><mrow><mi>c</mi><mi>a</mi><mi>l</mi><mi>c</mi></mrow></msub><mrow><mo>(</mo><mrow><mi>h</mi><mi>k</mi><mi>l</mi></mrow><mo>)</mo></mrow></mrow><mo>|</mo></mrow></mrow><mo>]</mo></mrow></mrow><mrow><mrow><mo>[</mo><mrow><msub><mo>∑</mo><mrow><mi>h</mi><mi>k</mi><mi>l</mi></mrow></msub><msub><mi>F</mi><mrow><mi>o</mi><mi>b</mi><mi>s</mi></mrow></msub><mrow><mo>(</mo><mrow><mi>h</mi><mi>k</mi><mi>l</mi></mrow><mo>)</mo></mrow></mrow><mo>]</mo></mrow></mrow><mo>×</mo><mn>100</mn></mrow></math>, where <i>F</i>_<i>obs</i> and <i>F</i>_<i>calc</i> are the observed and calculated structure factors respectively.</p><p>^e R_free is equivalent to R_factor but 5% of the measured reflections have been excluded from refinement and set aside for cross validation.</p><p>Data collection and refinement statistics on the apo and complex structures of TS_VZV.</p

Stereo views of the TS_VZV and TS_HS active sites.

<p>Corresponding stereo views of the ligands and amino acids lining the TS active sites in the structures of (a) apo-TS_VZV with a phosphate ion, (b) TS_VZV with dUMP, (c) TS_HS with dUMP (PDB ID: 1HVY) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143947#pone.0143947.ref035" target="_blank">35</a>] and (d) TS_VZV with BVDU_P. The polar interactions between the amino acids and the different ligands are illustrated by orange dotted lines. 2F₀-F_C electron densities of the binding (e) BVDU_P and (f) dUMP with the surrounding hydrophobic amino acids are also shown (contoured at 1σ with carved = 2.0).</p