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- PDB-8ddh: Racemic mixture of FYF peptide reveals rippled beta-sheet -

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Basic information

Entry
Database: PDB / ID: 8ddh
TitleRacemic mixture of FYF peptide reveals rippled beta-sheet
ComponentsPHE-TYR-PHE
KeywordsPROTEIN FIBRIL / Rippled beta-sheet / Racemic peptide
Biological speciesSynthetic Construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.1 Å
AuthorsSawaya, M.R. / Hazari, A. / Eisenberg, D.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chem Sci / Year: 2022
Title: The rippled β-sheet layer configuration-a novel supramolecular architecture based on predictions by Pauling and Corey.
Authors: Amaruka Hazari / Michael R Sawaya / Niko Vlahakis / Timothy C Johnstone / David Boyer / Jose Rodriguez / David Eisenberg / Jevgenij A Raskatov /
Abstract: The rippled β-sheet is a peptidic structural motif related to but distinct from the pleated β-sheet. Both motifs were predicted in the 1950s by Pauling and Corey. The pleated β-sheet was since ...The rippled β-sheet is a peptidic structural motif related to but distinct from the pleated β-sheet. Both motifs were predicted in the 1950s by Pauling and Corey. The pleated β-sheet was since observed in countless proteins and peptides and is considered common textbook knowledge. Conversely, the rippled β-sheet only gained a meaningful experimental foundation in the past decade, and the first crystal structural study of rippled β-sheets was published as recently as this year. Noteworthy, the crystallized assembly stopped at the rippled β-dimer stage. It did not form the extended, periodic rippled β-sheet layer topography hypothesized by Pauling and Corey, thus calling the validity of their prediction into question. NMR work conducted since moreover shows that certain model peptides rather form pleated and not rippled β-sheets in solution. To determine whether the periodic rippled β-sheet layer configuration is viable, the field urgently needs crystal structures. Here we report on crystal structures of two racemic and one quasi-racemic aggregating peptide systems, all of which yield periodic rippled antiparallel β-sheet layers that are in excellent agreement with the predictions by Pauling and Corey. Our study establishes the rippled β-sheet layer configuration as a motif with general features and opens the road to structure-based design of unique supramolecular architectures.
History
DepositionJun 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1May 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: PHE-TYR-PHE


Theoretical massNumber of molelcules
Total (without water)4761
Polymers4761
Non-polymers00
Water543
1
A: PHE-TYR-PHE

A: PHE-TYR-PHE

A: PHE-TYR-PHE

A: PHE-TYR-PHE

A: PHE-TYR-PHE

A: PHE-TYR-PHE


Theoretical massNumber of molelcules
Total (without water)2,8536
Polymers2,8536
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation7_555-x+1/2,-y+1/2,-z1
crystal symmetry operation7_565-x+1/2,-y+3/2,-z1
crystal symmetry operation7_545-x+1/2,-y-1/2,-z1
Unit cell
Length a, b, c (Å)22.020, 9.570, 25.840
Angle α, β, γ (deg.)90.000, 102.350, 90.000
Int Tables number15
Space group name H-MC12/c1

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Components

#1: Protein/peptide PHE-TYR-PHE


Mass: 475.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic Construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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

CrystalDescription: needle
Crystal growTemperature: 298 K / Method: batch mode / Details: hexafluoroisopropanol and water

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.1→12.62 Å / Num. obs: 1905 / % possible obs: 91.8 % / Redundancy: 16.017 % / Biso Wilson estimate: 7.996 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.084 / Χ2: 0.946 / Net I/σ(I): 25.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.138.2720.15510.67810.9860.16657
1.13-1.1610.8320.16112.831010.9970.17161.6
1.16-1.212.5740.1416.071360.9940.14780.5
1.2-1.2415.720.11920.561250.9980.12397.7
1.24-1.2817.4770.12718.231550.9980.131100
1.28-1.3315.7960.11922.011420.9980.12398.6
1.33-1.3917.1550.1123.111290.9980.11494.9
1.39-1.4517.1950.11722.591180.9980.121100
1.45-1.5217.7920.09624.681250.9970.09998.4
1.52-1.617.5810.09727.861170.9980.10198.3
1.6-1.718.1850.09429.71080.9960.097100
1.7-1.8117.9890.07834.1950.9990.081100
1.81-1.9615.2410.08731.231080.9990.0999.1
1.96-2.1518.6360.07337.76770.9990.075100
2.15-2.417.7310.06838.03930.9990.07100
2.4-2.7717.2580.07636.28620.9990.079100
2.77-3.3916.3330.06340.45600.9990.065100
3.39-4.816.0410.06438.984910.06698
4.8-12.62150.07335.98240.9980.076100

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXrefinement
PDB_EXTRACT3.27data extraction
SHELXDphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→12.62 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.0676 179 10 %
all0.0552 --
obs0.0552 1621 91.8 %
Displacement parametersBiso max: 70.54 Å2 / Biso mean: 6.5074 Å2 / Biso min: 3.47 Å2
Refinement stepCycle: LAST / Resolution: 1.1→12.62 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms35 0 0 3 38
LS refinement shellResolution: 1.1→1.23 Å
RfactorNum. reflection% reflection
Rfree0.088 --
Rwork0.109 --
obs-374 72.2 %

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