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- PDB-8ddf: Quasi-racemic mixture of L-FWF and D-FYF peptide reveals rippled ... -

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Basic information

Entry
Database: PDB / ID: 8ddf
TitleQuasi-racemic mixture of L-FWF and D-FYF peptide reveals rippled beta-sheet
Components
  • DPN-DTY-DPN
  • PHE-TRP-PHE
KeywordsPROTEIN FIBRIL / Rippled beta-sheet / quasi-racemic peptides
Function / homology1,1,1,3,3,3-hexafluoropropan-2-ol / polypeptide(D)
Function and homology information
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHE-TRP-PHE
B: DPN-DTY-DPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,3104
Polymers9742
Non-polymers3362
Water181
1
A: PHE-TRP-PHE
B: DPN-DTY-DPN
hetero molecules

A: PHE-TRP-PHE
B: DPN-DTY-DPN
hetero molecules

A: PHE-TRP-PHE
B: DPN-DTY-DPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,93112
Polymers2,9226
Non-polymers1,0086
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_455x-1,y,z1
Unit cell
Length a, b, c (Å)9.660, 26.260, 11.630
Angle α, β, γ (deg.)90.000, 95.120, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein/peptide PHE-TRP-PHE


Mass: 498.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Polypeptide(D) DPN-DTY-DPN


Mass: 475.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CFH / 1,1,1,3,3,3-hexafluoropropan-2-ol


Mass: 168.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2F6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.51 Å3/Da / Density % sol: 18.45 % / Description: needle
Crystal growTemperature: 298 K / Method: batch mode / Details: Hexafluoroisopropanol, 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: Mar 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.1→13.13 Å / Num. obs: 2232 / % possible obs: 93.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 308 / CC1/2: 0.943 / % possible all: 66.1

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→13.13 Å / SU ML: 0.0835 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 18.111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1274 224 10.08 %
Rwork0.0915 1999 -
obs0.0952 2223 93.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.86 Å2
Refinement stepCycle: LAST / Resolution: 1.1→13.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms82 0 10 1 93
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166120
X-RAY DIFFRACTIONf_angle_d2.756172
X-RAY DIFFRACTIONf_chiral_restr0.10788
X-RAY DIFFRACTIONf_plane_restr0.010516
X-RAY DIFFRACTIONf_dihedral_angle_d17.476132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.390.15641040.144926X-RAY DIFFRACTION87.21
1.39-13.130.12031200.07831073X-RAY DIFFRACTION99.5

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