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- PDB-9dyz: VVGG(DVA)(DVA)GG, a cyclic peptide of mixed chirality -

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Basic information

Entry
Database: PDB / ID: 9dyz
TitleVVGG(DVA)(DVA)GG, a cyclic peptide of mixed chirality
ComponentsVVGG(DVA)(DVA)GG
KeywordsPROTEIN FIBRIL / mixed chirality peptide
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.101 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
AAA: VVGG(DVA)(DVA)GG


Theoretical massNumber of molelcules
Total (without water)6431
Polymers6431
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.590, 10.360, 4.830
Angle α, β, γ (deg.)98.280, 95.066, 100.372
Int Tables number2
Space group name H-MP-1

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Components

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


Mass: 642.746 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.: 2 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 298 K / Method: batch mode / Details: dimethylsulfoxide 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: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.1→9.53 Å / Num. obs: 1113 / % possible obs: 82.7 % / Redundancy: 5.6 % / CC1/2: 0.991 / Rmerge(I) obs: 0.144 / Rrim(I) all: 0.159 / Net I/σ(I): 7.14
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.1-1.150.469690.8850.531
1.15-1.220.4051160.8580.4511
1.22-1.290.281360.9690.3091
1.29-1.380.351370.940.3861
1.38-1.490.241420.980.2661
1.49-1.630.1761270.970.1931
1.63-1.830.1741060.9740.1921
1.83-2.110.133950.9860.1491
2.11-2.580.122910.9910.1341
2.58-3.650.099610.9850.111
3.65-9.530.109330.9930.1191

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALE20220820data scaling
XDS20220820data reduction
SHELXT2018/2phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.101→9.528 Å / Cor.coef. Fo:Fc: 0.992 / Cor.coef. Fo:Fc free: 0.99 / Cross valid method: FREE R-VALUE / ESU R: 0.032 / ESU R Free: 0.029
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.112 112 10.072 %
Rwork0.0932 1000 -
all0.095 --
obs-1112 82.8 %
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: 5.379 Å2
Baniso -1Baniso -2Baniso -3
1-0.551 Å2-0.362 Å20.021 Å2
2---0.49 Å20.554 Å2
3----0.106 Å2
Refinement stepCycle: LAST / Resolution: 1.101→9.528 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms44 0 0 2 46
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01242
X-RAY DIFFRACTIONr_bond_other_d0.0290.01748
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.52954
X-RAY DIFFRACTIONr_angle_other_deg1.2211.548106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg2.322152
X-RAY DIFFRACTIONr_chiral_restr0.0960.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0242
X-RAY DIFFRACTIONr_gen_planes_other00.026
X-RAY DIFFRACTIONr_nbd_refined0.0630.21
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0110.21
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0050.21
X-RAY DIFFRACTIONr_mcbond_it0.9440.51430
X-RAY DIFFRACTIONr_mcbond_other0.8170.50628
X-RAY DIFFRACTIONr_mcangle_it1.0530.77634
X-RAY DIFFRACTIONr_mcangle_other1.0570.77634
X-RAY DIFFRACTIONr_scbond_it0.5410.53712
X-RAY DIFFRACTIONr_scbond_other0.520.54813
X-RAY DIFFRACTIONr_scangle_it0.4380.79320
X-RAY DIFFRACTIONr_scangle_other0.6180.821
X-RAY DIFFRACTIONr_lrange_it1.4343.97610
X-RAY DIFFRACTIONr_rigid_bond_restr2.406390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.101-1.2290.145210.1531850.1523880.9860.98353.09280.128
1.229-1.4150.188290.1252600.1313120.970.98992.62820.104
1.415-1.7230.113290.0892580.0913000.9950.99595.66670.084
1.723-2.3980.1210.0771900.0792190.9940.99696.3470.082
2.398-9.5280.086120.0731070.0751220.9950.99797.5410.086

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