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- PDB-9dyy: peptide of mixed chirality, VVGG(DVA)(DVA), assembles into a ripp... -

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Basic information

Entry
Database: PDB / ID: 9dyy
Titlepeptide of mixed chirality, VVGG(DVA)(DVA), assembles into a rippled beta sheet
ComponentsVVGG(DVA)(DVA)
KeywordsPROTEIN FIBRIL / rippled beta sheet / racemic mixture
Function / homology1,1,1,3,3,3-hexafluoropropan-2-ol
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.3 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: VVGG(DVA)(DVA)
B: VVGG(DVA)(DVA)
C: VVGG(DVA)(DVA)
D: VVGG(DVA)(DVA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,7798
Polymers2,1074
Non-polymers6724
Water00
1
A: VVGG(DVA)(DVA)
B: VVGG(DVA)(DVA)
C: VVGG(DVA)(DVA)
D: VVGG(DVA)(DVA)
hetero molecules

A: VVGG(DVA)(DVA)
B: VVGG(DVA)(DVA)
C: VVGG(DVA)(DVA)
D: VVGG(DVA)(DVA)
hetero molecules

A: VVGG(DVA)(DVA)
B: VVGG(DVA)(DVA)
C: VVGG(DVA)(DVA)
D: VVGG(DVA)(DVA)
hetero molecules

A: VVGG(DVA)(DVA)
B: VVGG(DVA)(DVA)
C: VVGG(DVA)(DVA)
D: VVGG(DVA)(DVA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,11532
Polymers8,42616
Non-polymers2,68916
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)33.120, 44.270, 9.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
VVGG(DVA)(DVA)


Mass: 526.650 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-CFH / 1,1,1,3,3,3-hexafluoropropan-2-ol


Mass: 168.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2F6O
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: 1.63 Å3/Da / Density % sol: 24.32 %
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: Oct 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.3→26.52 Å / Num. obs: 3738 / % possible obs: 99.5 % / Redundancy: 5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.241 / Rrim(I) all: 0.271 / Net I/σ(I): 3.68
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.3-1.371.9865310.3432.2211
1.37-1.451.234710.6381.3711
1.45-1.551.0124990.7281.1251
1.55-1.680.7024410.9020.7851
1.68-1.840.5844220.9080.6531
1.84-2.060.2643690.9840.2951
2.06-2.370.1883380.980.211
2.37-2.910.1732890.9940.1971
2.91-4.110.1332280.9880.1531
4.11-26.520.0771500.9980.0911

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XSCALE20241002data scaling
XDS20241002data reduction
SHELXD2013/2phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.3→26.52 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.986 / SU B: 4.125 / SU ML: 0.068 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.06
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT FILE
RfactorNum. reflection% reflection
Rfree0.188 374 9.997 %
Rwork0.181 --
obs-3738 99.5 %
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: 12.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.393 Å20 Å20 Å2
2--0.089 Å20 Å2
3---1.305 Å2
Refinement stepCycle: LAST / Resolution: 1.3→26.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms148 0 40 0 188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.013180
X-RAY DIFFRACTIONr_bond_other_d0.0040.016188
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.605244
X-RAY DIFFRACTIONr_angle_other_deg1.351.628412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.311516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg4.0851012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr1.8370.244
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02136
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0232
X-RAY DIFFRACTIONr_nbd_refined0.1260.227
X-RAY DIFFRACTIONr_nbd_other0.160.249
X-RAY DIFFRACTIONr_nbtor_refined0.1470.298
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.28
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2510.92992
X-RAY DIFFRACTIONr_mcbond_other3.2360.9393
X-RAY DIFFRACTIONr_mcangle_it4.2321.64296
X-RAY DIFFRACTIONr_mcangle_other4.2251.64297
X-RAY DIFFRACTIONr_scbond_it11.3331.64888
X-RAY DIFFRACTIONr_scbond_other11.0621.62986
X-RAY DIFFRACTIONr_scangle_it16.3712.91148
X-RAY DIFFRACTIONr_scangle_other16.1592.892146
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.753368
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.45 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.342 102 -
Rwork0.316 922 -
obs--99.9 %

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