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

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Basic information

Entry
Database: PDB / ID: 9dyw
Titleracemic mixture of peptide VVGGVV forms rippled sheets
ComponentsVVGGVV
KeywordsPROTEIN FIBRIL / rippled sheet / racemic mixture
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

Downloads & links

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Assembly

Deposited unit
A: VVGGVV
B: VVGGVV


Theoretical massNumber of molelcules
Total (without water)1,0572
Polymers1,0572
Non-polymers00
Water18010
1
A: VVGGVV

A: VVGGVV

A: VVGGVV

A: VVGGVV


Theoretical massNumber of molelcules
Total (without water)2,1154
Polymers2,1154
Non-polymers00
Water724
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
2
B: VVGGVV

B: VVGGVV

B: VVGGVV

B: VVGGVV


Theoretical massNumber of molelcules
Total (without water)2,1154
Polymers2,1154
Non-polymers00
Water724
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)22.950, 15.490, 9.520
Angle α, β, γ (deg.)88.665, 92.764, 103.947
Int Tables number2
Space group name H-MP-1

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Components

#1: Protein/peptide VVGGVV


Mass: 528.642 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.55 Å3/Da / Density % sol: 20.72 % / Description: needle
Crystal growTemperature: 298 K / Method: batch mode / pH: 3 / Details: 20% hexafluoroisopropanol in water

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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: Oct 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.1→15.03 Å / Num. obs: 4615 / % possible obs: 89.4 % / Redundancy: 2.7 % / CC1/2: 0.981 / Rmerge(I) obs: 0.155 / Rrim(I) all: 0.19 / Net I/σ(I): 3.96
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.1-1.130.282110.8530.3621
1.13-1.160.2623030.9270.3321
1.16-1.190.2283000.9610.2861
1.19-1.230.2563120.9060.3181
1.23-1.270.233080.9260.2881
1.27-1.320.2433040.8770.31
1.32-1.360.2363070.9160.291
1.36-1.420.222750.920.2711
1.42-1.480.1972760.9360.2451
1.48-1.560.2022690.9450.2481
1.56-1.640.2112570.8940.2591
1.64-1.740.1712310.9650.2121
1.74-1.860.1722330.9580.211
1.86-2.010.1612090.9490.1971
2.01-2.20.161960.9630.1941
2.2-2.460.1431710.9550.1731
2.46-2.840.1371530.980.1731
2.84-3.480.1441370.9770.1731
3.48-4.920.1161100.9860.1441
4.92-15.030.112530.9920.141

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALE20230630data scaling
XDS20230630data reduction
SHELXD2013/2phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→15.03 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.632 / SU ML: 0.014 / Cross valid method: FREE R-VALUE / ESU R: 0.029 / ESU R Free: 0.029
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1672 462 10.011 %
Rwork0.1508 4153 -
all0.152 --
obs-4615 89.438 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 6.533 Å2
Baniso -1Baniso -2Baniso -3
1-0.006 Å2-0.111 Å2-0.03 Å2
2--0.524 Å20.157 Å2
3----0.533 Å2
Refinement stepCycle: LAST / Resolution: 1.1→15.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms74 0 0 10 84
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01377
X-RAY DIFFRACTIONr_bond_other_d0.0070.01796
X-RAY DIFFRACTIONr_angle_refined_deg1.9581.611107
X-RAY DIFFRACTIONr_angle_other_deg1.3641.628215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.268512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.558159
X-RAY DIFFRACTIONr_chiral_restr0.0620.29
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0293
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211
X-RAY DIFFRACTIONr_nbd_refined0.0720.212
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1410.275
X-RAY DIFFRACTIONr_nbtor_refined0.1340.243
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.254
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0620.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0270.22
X-RAY DIFFRACTIONr_nbd_other0.0960.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.27
X-RAY DIFFRACTIONr_mcbond_it0.4920.58848
X-RAY DIFFRACTIONr_mcbond_other0.4970.58647
X-RAY DIFFRACTIONr_mcangle_it0.6540.89157
X-RAY DIFFRACTIONr_mcangle_other0.6480.89258
X-RAY DIFFRACTIONr_scbond_it0.6180.68929
X-RAY DIFFRACTIONr_scbond_other0.6150.69329
X-RAY DIFFRACTIONr_scangle_it0.8061.00949
X-RAY DIFFRACTIONr_scangle_other0.8061.01149
X-RAY DIFFRACTIONr_lrange_it1.2368.72978
X-RAY DIFFRACTIONr_lrange_other1.248.63777
X-RAY DIFFRACTIONr_rigid_bond_restr1.3363173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.2290.1741120.2011002X-RAY DIFFRACTION76.4585
1.229-1.4180.2011200.1781080X-RAY DIFFRACTION92.6641
1.418-1.7330.1621010.138915X-RAY DIFFRACTION94.4238
1.733-2.4340.157820.127740X-RAY DIFFRACTION95.8042
2.434-15.030.158470.147416X-RAY DIFFRACTION97.8858

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