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Unified Data Resource for Cryo-EM
[chapter]
2010
Methods in Enzymology
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For structures with regular point or helical symmetry, coordinates for one asymmetric unit may be deposited along with transformation matrices to build the assembly (Lawson et al., 2008) . ...
For structures with regular point or helical symmetry, coordinates are given for the asymmetric unit along with a set of transformation matrices to build the biological assembly (Lawson et al., 2008) ...
doi:10.1016/s0076-6879(10)83004-6
pmid:20888470
pmcid:PMC2966391
fatcat:ncsypzwkdvh6dopessk56ubpaq
Comparing cryo-EM structures
2018
Journal of Structural Biology
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EM Data Bank (EMDB) now holds more than 6500 cryo-EM density maps, and Protein Data Bank (PDB) holds more than 2500 structure coordinates, contributed by the growing cryo-EM community (Patwardhan and Lawson ...
A total of 66 maps and 142 models were contributed, each with supporting details about the workflow from benchmark to final result ( [dataset] Lawson et al., 2017; [dataset] Lawson et al., 2018) . ...
doi:10.1016/j.jsb.2018.10.004
pmid:30321594
pmcid:PMC6464812
fatcat:6ssyvddm55d47gvzkynsuqeb6u
Developing Community Resources for Nucleic Acid Structures
2022
Life
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NtC class BB00 (l acterizes the B form, AA00 (center) A form in both DNA and RNA, and NANT (right) a classified dinucleotides. ...
doi:10.3390/life12040540
pmid:35455031
pmcid:PMC9031032
fatcat:2e5nwcxpk5dvdff34brexevwty
The data universe of structural biology
2020
IUCrJ
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et al., 2016; Lawson & Chiu, 2018) . ...
and the National Center for Macromolecular Imaging (NCMI) initiated a collaboration to ensure that data archiving and validation standards for cryo-EM maps and models are coordinated internationally (Lawson ...
doi:10.1107/s205225252000562x
pmid:32695409
pmcid:PMC7340255
fatcat:mnh7usf2zfg3rljrw77gzy4k4a
Evolving data standards for cryo-EM structures
2020
Structural Dynamics
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L. Lawson and W. Chiu, J. Struct. Biol. 204(3), 523-526 (2018). ...
Wah Chiu, Cathy Lawson, Paul Adams First pass analyses of models and data submitted to the 2016 Model Challenge #
Year
Title/location
Organizers
Description
Key outcomes
Model Workshop, CA,
USA ...
doi:10.1063/1.5138589
pmid:32002441
pmcid:PMC6980868
fatcat:rzpnh3prwfh75fondzo27zjfgy
Letter from the Editorial Team
1999
Journal of International Business Studies
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We are pleased to announce that, effective immediately, new procedures for submission and review of papers are in place for JIBS. We have devised these new procedures to provide an expedited and efficient review process that is author-friendly and reviewer-friendly. The new procedures use electronic files and communications extensively throughout the submission-review process, and we expect them to reduce the turn-aroundtime at several points. We will be reportingthe results of the new procedures in due course.
doi:10.1057/jibs.1999.16
fatcat:vgzml2zewfhgxkpgkomymgipuy
Children's active commuting to school: current knowledge and future directions
2008
Preventing Chronic Disease
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Driven largely by international declines in rates of walking and bicycling to school and the noted health benefits of physical activity for children, research on children's active commuting to school has expanded rapidly during the past 5 years. We summarize research on predictors and health consequences of active commuting to school and outline and evaluate programs specific to children's walking and bicycling to school. Literature on children's active commuting to school published before June
pmid:18558018
pmcid:PMC2483568
fatcat:cxcx5ug3irhuxnbbc5ql5drblq
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... 2007 was compiled by searching PubMed, PsycINFO, and the National Transportation Library databases; conducting Internet searches on program-based activities; and reviewing relevant transportation journals published during the last 4 years. Children who walk or bicycle to school have higher daily levels of physical activity and better cardiovascular fitness than do children who do not actively commute to school. A wide range of predictors of children's active commuting behaviors was identified, including demographic factors, individual and family factors, school factors (including the immediate area surrounding schools), and social and physical environmental factors. Safe Routes to School and the Walking School Bus are 2 public health efforts that promote walking and bicycling to school. Although evaluations of these programs are limited, evidence exists that these activities are viewed positively by key stakeholders and have positive effects on children's active commuting to school. Future efforts to promote walking and bicycling to school will be facilitated by building on current research, combining the strengths of scientific rigor with the predesign and postdesign provided by intervention activities, and disseminating results broadly and rapidly.
Approaches toward the Directed Design of a Vaccine againstBorrelia burgdorferi
2002
Journal of Infectious Diseases
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The tryptophan repressor sequence is highly conserved among theEnterobacteriaceae
1994
Nucleic Acids Research
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Trp aporepressor binds the corepressor, L-tryptophan, to form a holorepressor complex, which binds trp operator DNA tightly, and inhibits transcription of the tryptophan biosynthetic operon. ...
Italicized print corresponds to amino acids with side chains involved in binding to corepressor, L-tryptophan. ...
The other subunit (gray coil) and the two L-typtophan corpressor ligands (gray stick model) are shown for reference. ...
doi:10.1093/nar/22.10.1821
pmid:8208606
pmcid:PMC308080
fatcat:v767rzqnpzhg3opyszqjixm5fu
Environment-dependent long-range structural distortion in a temperature-sensitive point mutant
2011
Protein Science
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Extensive environment-dependent rearrangement of the helix-turn-helix DNA recognition region and adjacent L-tryptophan binding pocket is reported in the crystal structure of dimeric E. coli trp aporepressor ...
A tris cation occupying one L-tryptophan binding pocket in the L75F apoTrpR structure is also shown (compare dotted surface for tris in (B) and for L-tryptophan in Fig. 1). ...
In the wt conformer the absence of a sidechain at Gly85 accommodates the L-tryptophan indole 18, 30 ; therefore, L-tryptophan binding would be incompatible with the distorted mutant conformation. ...
doi:10.1002/pro.759
pmid:22057811
pmcid:PMC3323781
fatcat:qdvivcoesjgdvbpovftn7axj5i
Structural Investigation ofBorrelia burgdorferiOspB, a BactericidalFab Target
2005
Journal of Biological Chemistry
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The OspB-CT crystal form was obtained by mixing 4 l of freshly purified protein with 4 l of 25% PEG550MME, 0.1 M Bicine, 0.1 M sodium bromide, 0.03 M sodium citrate, pH 9.5, and equilibrating at 295 K ...
Crystals of the OspB-CT ϩ H6831 Fab complex were obtained by mixing 4 l of complex with 4 l of either: (a) 25% PEG 3350, 0.2 M sodium citrate, pH 5.6, (b) 25% PEG 3350, 5% isopropyl alcohol, 0.2 M sodium ...
doi:10.1074/jbc.m412842200
pmid:15713683
fatcat:wx3w6olhgvaoriuqdyy6itkdtm
E. coli trp Repressor Forms a Domain-Swapped Array in Aqueous Alcohol
2004
Structure
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Flexible N-terminal arms mediate surface adjacent to and involving the HTH (Figure 1B) association between dimers bound to tandem DNA (Lawson and Carey, 1993). TrpR dimers also associate sites. ...
Each subunit is represented as an N and C segment connected by flexible linker L. ...
Sidechains (labeled) and L-tryptophan (unlabeled) are shown in space-fill.
Table 1 . ...
doi:10.1016/j.str.2004.03.019
pmid:15274929
pmcid:PMC3228604
fatcat:6dnpgbqtrbc25mtjllhwthyj2m
Structure of theEscherichia coliRNA polymerase α subunit C-terminal domain
2010
Acta Crystallographica Section D: Biological Crystallography
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The L-test, based on deviations in local intensities (Padilla & Yeates, 2003) , yielded results that were consistent with pseudomerohedral twinning: |L| = 0.43 (expected value of 0.500 for untwinned and ...
0.375 for a perfect twin) and L 2 = 0.26 (0.333 for untwinned and 0.200 for a perfect twin). ...
doi:10.1107/s0907444910018470
pmid:20606261
pmcid:PMC2897699
fatcat:t2doshpmejelfnzfzyhog2ggve
Representation of viruses in the remediated PDB archive
2008
Acta Crystallographica Section D: Biological Crystallography
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D64, 874-882 Lawson et al. Representation of viruses in the PDB 877
et al. Representation of viruses in the PDB Acta Cryst. (2008). D64, 874-882
Figure 4
et al. ...
doi:10.1107/s0907444908017393
pmid:18645236
pmcid:PMC2677383
fatcat:jw6vevz23nghdmc4i66634yqje
Structure of catabolite activator protein with cobalt(II) and sulfate
2014
Acta Crystallographica Section F Structural Biology Communications
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Introduction CAP (catabolite activator protein) is a DNA-binding protein and transcription activator that recruits RNA polymerase to more than 100 genes in Escherichia coli (Busby & Ebright, 1999; Lawson ...
Activating region 1 (AR1), located on the C-terminal domain, attracts a flexibly tethered RNAP subunit C-terminal domain to bind to a DNA site adjacent to CAP (Benoff et al., 2002; Lawson et al., 2004 ...
doi:10.1107/s2053230x14005366
pmid:24817710
pmcid:PMC4014319
fatcat:3f6x6mc6q5dbhn2xoglefgf56a
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