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- PDB-9dyx: racemic mixture of peptide VVGGVV forms rippled sheets -

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Basic information

Entry
Database: PDB / ID: 9dyx
Titleracemic mixture of peptide VVGGVV forms rippled sheets
ComponentsVVGGVV-amidated racemic mixture
KeywordsPROTEIN FIBRIL / rippled beta sheet / racemic mixture
Function / homologypentafluoropropanoic acid
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.1 Å
AuthorsSawaya, M.R. / Raskatov, J.A. / Hazari, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG070895 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG048120 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG074954 United States
CitationJournal: Chem Sci / Year: 2025
Title: Formation of rippled beta-sheets from mixed chirality linear and cyclic peptides-new structural motifs based on the pauling-corey rippled beta-sheet.
Authors: Hazari, A. / Sawaya, M.R. / Lee, H. / Sajimon, M. / Kim, H. / Goddard Iii, W.A. / Eisenberg, D. / Raskatov, J.A.
History
DepositionOct 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VVGGVV-amidated racemic mixture
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6912
Polymers5271
Non-polymers1641
Water00
1
A: VVGGVV-amidated racemic mixture
hetero molecules

A: VVGGVV-amidated racemic mixture
hetero molecules

A: VVGGVV-amidated racemic mixture
hetero molecules

A: VVGGVV-amidated racemic mixture
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,7638
Polymers2,1074
Non-polymers6564
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_535x,y-2,z1
Unit cell
Length a, b, c (Å)12.290, 12.460, 11.780
Angle α, β, γ (deg.)76.000, 89.290, 88.490
Int Tables number2
Space group name H-MP-1
Space group name Hall-P1
Symmetry operation#1: x,y,z
#2: -x,-y,-z

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Components

#1: Protein/peptide VVGGVV-amidated racemic mixture


Mass: 526.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-YWK / pentafluoropropanoic acid


Mass: 164.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3HF5O2
Has ligand of interestN
Has protein modificationY

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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: 1.66 Å3/Da / Density % sol: 25.81 %
Crystal growTemperature: 298 K / Method: batch mode / Details: hexafluoroisopropanol and water / PH range: 3-4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.1→12.29 Å / Num. obs: 2331 / % possible obs: 84.7 % / Redundancy: 1.6 % / Biso Wilson estimate: 46.91 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.113 / Net I/σ(I): 3.82
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.1-1.130.4271020.7640.6041
1.13-1.160.1611170.9890.2281
1.16-1.190.2921620.9270.4131
1.19-1.230.221650.9440.3111
1.23-1.270.2051500.9550.2891
1.27-1.320.1821580.9590.2571
1.32-1.370.1811640.9560.2551
1.37-1.420.1331380.9810.1871
1.42-1.490.161430.9450.2261
1.49-1.560.0881430.9920.1241
1.56-1.640.1421190.9590.2011
1.64-1.740.0741350.980.1051
1.74-1.860.0941020.9770.1331
1.86-2.010.0711020.9920.11
2.01-2.20.0991020.9530.141
2.2-2.460.0951080.9560.1351
2.46-2.840.095690.9820.1341
2.84-3.480.099690.90.141
3.48-4.930.066530.9930.0931
4.93-12.290.033300.9980.0471

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XSCALE20230630data scaling
XDS20230630data reduction
SHELXD2013/2phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→12.29 Å / SU ML: 0.0639 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.4667
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1775 232 9.99 %
Rwork0.1789 2090 -
obs0.1788 2322 84.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.06 Å2
Refinement stepCycle: LAST / Resolution: 1.1→12.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29 0 18 0 47
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012244
X-RAY DIFFRACTIONf_angle_d1.933661
X-RAY DIFFRACTIONf_chiral_restr0.10227
X-RAY DIFFRACTIONf_plane_restr0.0036
X-RAY DIFFRACTIONf_dihedral_angle_d17.03519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.390.26831060.2731958X-RAY DIFFRACTION77.33
1.39-12.290.15951260.15921132X-RAY DIFFRACTION91.76

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