Literature DB >> 26208179

Correction: The Crystal Structure and Small-Angle X-Ray Analysis of CsdL/TcdA Reveal a New tRNA Binding Motif in the MoeB/E1 Superfamily.

Miguel López-Estepa, Ana Ardá, Martin Savko, Adam Round, William E Shepard, Marta Bruix, Miquel Coll, Francisco J Fernández, Jesús Jiménez-Barbero, M Cristina Vega.   

Abstract

Entities:  

Year:  2015        PMID: 26208179      PMCID: PMC4514599          DOI: 10.1371/journal.pone.0134070

Source DB:  PubMed          Journal:  PLoS One        ISSN: 1932-6203            Impact factor:   3.240


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There are multiple errors in Table 1. Please see the corrected Table 1 here.
Table 1

Crystallographic data processing and refinement statistics.

TcdA-ATPTcdA-AMP
PDB code4D794D7A
Data collection
Wavelength (Å)0.97950.9801
Resolution range (Å)41.13–1.77 (1.83–1.77)41.14–1.80 (1.86–1.80)
Space group P 1 21 1 P 1 21 1
Unit cell dimensions
a, b, c (Å)65.3, 96.7, 82.865.7, 97.2, 83.2
β (°), α = γ = 90°90, 111.2, 9090, 111.6, 90
Total reflections312,887 (11,351)351,361 (33,129)
Unique reflections89,883 (5907)87,219 (8261)
Multiplicity3.5 (1.9)4.0 (4.0)
Completeness (%)95.96 (63.90)97.14 (92.68)
Mean I/σ(I)18.97 (3.75)19.93 (4.05)
Wilson B-factor23.9521.59
R-merge0.08388 (0.663)0.04687 (0.412)
R-meas a 0.097970.05407
CC1/2 b 0.995 (0.556)0.999 (0.0.875)
CC* c 0.999 (0.846)1.000 (0.966)
Refinement
R-work0.1416 (0.2994)0.1396 (0.1839)
R-free0.1833 (0.3236)0.1768 (0.2350)
# non-H atoms81678064
# Protein atoms74847411
# Ligand atoms17246
# Water511607
Protein residues996974
RMS(bonds) (Å)0.0110.007
RMS(angles) (°)1.4301.01
Ramachandran analysis
Favored/Allowed/Outlier (%)98.0/2.0/0.098.0/2.0/0.0
Clashscore1.881.93
Average B-factor (Å2)34.4032.10
 Protein33.6031.50
 Ligands60.8049.70
 Solvent38.0037.20

aRmeas = Σhkl (n/n-1)1/2 Σi |Ii(hkl)-| / ΣΣi Ii(hkl); where i is the ith measurement of reflection (hkl) and is the average over symmetry related observations of a unique reflection (hkl).

bCC1/2 is the Pearson correlation coefficient calculated between two random half data sets.

cCC* is the CC of the full data set against the true intensities, estimated from CC* = [2 CC1/2/(1+CC1/2)]1/2.

aRmeas = Σhkl (n/n-1)1/2 Σi |Ii(hkl)-| / ΣΣi Ii(hkl); where i is the ith measurement of reflection (hkl) and is the average over symmetry related observations of a unique reflection (hkl). bCC1/2 is the Pearson correlation coefficient calculated between two random half data sets. cCC* is the CC of the full data set against the true intensities, estimated from CC* = [2 CC1/2/(1+CC1/2)]1/2. There is an error in the last sentence of the “TcdA crystallization, structure determination and refinement” subsection of the Materials and Methods. The correct sentence is: A data set for the AMP complex was collected to 1.80-Å resolution at the PROXIMA 2A beamline (Synchrotron SOLEIL, Paris, France). All the data sets were integrated with XDS [26] and scaled with Aimless [27] from the CCP4 suite of programs [28] (Table 1). There are errors in the fifth and sixth sentences of the “Crystal structure of TcdA” subsection of the Results and Discussion. The correct sentences are: To shed light onto the structural basis for the tRNA binding and ct6A synthetic properties of TcdA-ATP, we determined the crystal structure of E. coli TcdA (Table 1 and Fig 2) loaded with ATP to 1.77 Å resolution (R/Rfree values of 0.141/0.183) (Fig 3A) and AMP to 1.80 Å resolution (R/Rfreevalues of 0.139/0.176) (Fig 3B). The asymmetric unit contained four TcdA chains arranged in two independent dimers, with a solvent content of 39%.
  1 in total

1.  The crystal structure and small-angle X-ray analysis of CsdL/TcdA reveal a new tRNA binding motif in the MoeB/E1 superfamily.

Authors:  Miguel López-Estepa; Ana Ardá; Martin Savko; Adam Round; William E Shepard; Marta Bruix; Miquel Coll; Francisco J Fernández; Jesús Jiménez-Barbero; M Cristina Vega
Journal:  PLoS One       Date:  2015-04-21       Impact factor: 3.240

  1 in total

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