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- PDB-7n2h: X-Ray structure of a sequence variant of a repeat segment of the ... -

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Basic information

Entry
Database: PDB / ID: 7n2h
TitleX-Ray structure of a sequence variant of a repeat segment of the yeast prion New1p
Componentsprion New1p
KeywordsPROTEIN FIBRIL / amyloid / prion / New1p
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.102 Å
AuthorsRichards, L.S. / Flores, M.D. / Zee, C.T. / Glynn, C. / Gallagher-Jones, M. / Sawaya, M.R.
Funding support United States, Brazil, Spain, 13items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-1548924 United States
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128867 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM136508 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136614 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM007185 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI143368 United States
Sao Paulo Research Foundation (FAPESP)16/24191-8 United States
Sao Paulo Research Foundation (FAPESP)17/13485-3 Brazil
Spanish Ministry of Science, Innovation, and UniversitiesBES-2015-071397 United States
Spanish Ministry of Economy and CompetitivenessPGC2018-101370-B-100, Spain
Spanish Ministry of Economy and CompetitivenessMDM2014-0435-01 Spain
Other government2017SGR- 1192 Spain
CitationJournal: ACS Bio Med Chem Au / Year: 2023
Title: Fragment-Based Phasing of Peptidic Nanocrystals by MicroED.
Authors: Logan S Richards / Maria D Flores / Claudia Millán / Calina Glynn / Chih-Te Zee / Michael R Sawaya / Marcus Gallagher-Jones / Rafael J Borges / Isabel Usón / Jose A Rodriguez /
Abstract: Electron diffraction (MicroED/3DED) can render the three-dimensional atomic structures of molecules from previously unamenable samples. The approach has been particularly transformative for peptidic ...Electron diffraction (MicroED/3DED) can render the three-dimensional atomic structures of molecules from previously unamenable samples. The approach has been particularly transformative for peptidic structures, where MicroED has revealed novel structures of naturally occurring peptides, synthetic protein fragments, and peptide-based natural products. Despite its transformative potential, MicroED is beholden to the crystallographic phase problem, which challenges its determination of structures. ARCIMBOLDO, an automated, fragment-based approach to structure determination, eliminates the need for atomic resolution, instead enforcing stereochemical constraints through libraries of small model fragments, and discerning congruent motifs in solution space to ensure validation. This approach expands the reach of MicroED to presently inaccessible peptide structures including fragments of human amyloids, and yeast and mammalian prions. For electron diffraction, fragment-based phasing portends a more general phasing solution with limited model bias for a wider set of chemical structures.
History
DepositionMay 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: prion New1p


Theoretical massNumber of molelcules
Total (without water)8151
Polymers8151
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.200, 27.200, 4.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein/peptide prion New1p


Mass: 814.800 Da / Num. of mol.: 1 / Fragment: repeat segment / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.27 Å3/Da / Density % sol: 2.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 20% MPD, 0.1 M sodium acetate, pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.05→13.6 Å / Num. obs: 1793 / % possible obs: 90.2 % / Redundancy: 2.585 % / Biso Wilson estimate: 6.909 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.161 / Rrim(I) all: 0.197 / Χ2: 0.774 / Net I/σ(I): 4.13 / Num. measured all: 4635
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.05-1.12.0390.3591.973142521540.8910.44761.1
1.1-1.162.4720.3272.776132762480.8650.39889.9
1.16-1.232.6650.2623.295572402090.9290.32387.1
1.23-1.322.70.2533.435752162130.9370.3198.6
1.32-1.462.6380.2473.866782622570.9020.29998.1
1.46-1.672.680.1614.786462562410.9770.19694.1
1.67-2.12.6780.1315.646242342330.9720.1699.6
2.1-13.62.6390.1146.436282512380.9710.13994.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.16-3549-000refinement
PDB_EXTRACT3.27data extraction
SHELXDphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.102→13.6 Å / SU ML: -0 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 21.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1606 136 10.03 %
Rwork0.1383 1220 -
obs0.1408 1356 83.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 24.25 Å2 / Biso mean: 7.7091 Å2 / Biso min: 2.99 Å2
Refinement stepCycle: final / Resolution: 1.102→13.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms58 0 0 2 60
Biso mean---17.8 -
Num. residues----6
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.1022-1.18720.3489180.262516754
1.1872-1.30660.2414220.22919272
1.3066-1.49550.1979310.195227794
1.4955-1.88330.1704320.1316292100
1.8833-13.60.1166330.0956292100

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