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- PDB-9dz1: VVGGVVGG cyclic peptide -

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Basic information

Entry
Database: PDB / ID: 9dz1
TitleVVGGVVGG cyclic peptide
ComponentsVVGGVVGG-cyclic
KeywordsPROTEIN FIBRIL / enantiopure crystal grown from a racemic mixture of cyclic peptide
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.102 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: VVGGVVGG-cyclic


Theoretical massNumber of molelcules
Total (without water)6431
Polymers6431
Non-polymers00
Water181
1
A: VVGGVVGG-cyclic

A: VVGGVVGG-cyclic

A: VVGGVVGG-cyclic

A: VVGGVVGG-cyclic


Theoretical massNumber of molelcules
Total (without water)2,5714
Polymers2,5714
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)21.100, 4.810, 18.870
Angle α, β, γ (deg.)90.000, 118.441, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide VVGGVVGG-cyclic


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.: 1 / Source method: isolated from a natural source / Formula: H2O
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: racemic peptide mixture, 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: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.1→16.593 Å / Num. obs: 656 / % possible obs: 83.7 % / Redundancy: 5.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.089 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.1-1.190.28730.960.3151
1.19-1.30.1881240.9850.2071
1.3-1.460.1651220.9820.1821
1.46-1.680.111160.9880.1221
1.68-2.060.08960.9970.0871
2.06-2.920.076760.9930.0861
2.92-16.5930.057490.9950.0641

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALE20220820data scaling
XDS20220820data reduction
SHELXT2018/2phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.102→16.593 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.979 / SU B: 2.603 / SU ML: 0.049 / Cross valid method: FREE R-VALUE / ESU R: 0.084 / ESU R Free: 0.051
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.1507 66 10.076 %
Rwork0.1351 589 -
all0.136 --
obs-655 83.974 %
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: 7.092 Å2
Baniso -1Baniso -2Baniso -3
1-0.098 Å20 Å2-0.375 Å2
2--0.498 Å20 Å2
3----0.119 Å2
Refinement stepCycle: LAST / Resolution: 1.102→16.593 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms44 0 0 1 45
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01144
X-RAY DIFFRACTIONr_bond_other_d0.0010.01748
X-RAY DIFFRACTIONr_angle_refined_deg0.9221.53560
X-RAY DIFFRACTIONr_angle_other_deg0.241.539108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.73958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg4.702154
X-RAY DIFFRACTIONr_chiral_restr0.0470.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0256
X-RAY DIFFRACTIONr_gen_planes_other00.028
X-RAY DIFFRACTIONr_mcbond_it1.2220.66732
X-RAY DIFFRACTIONr_mcbond_other1.2580.67330
X-RAY DIFFRACTIONr_mcangle_it1.2240.99240
X-RAY DIFFRACTIONr_mcangle_other1.2190.99340
X-RAY DIFFRACTIONr_scbond_it1.0210.69112
X-RAY DIFFRACTIONr_scbond_other0.9810.68313
X-RAY DIFFRACTIONr_scangle_it1.3571.03920
X-RAY DIFFRACTIONr_scangle_other1.3251.03321
X-RAY DIFFRACTIONr_lrange_it1.1061.8412
X-RAY DIFFRACTIONr_rigid_bond_restr1.396392
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
1.102-1.2320.342120.1981040.2092200.8540.91252.72730.187
1.232-1.4210.228180.1931680.1961870.9450.94699.46520.188
1.421-1.7370.239150.1421340.151570.9240.97294.90450.152
1.737-2.4430.169130.1341160.1371350.9690.98595.55560.153
2.443-16.5930.03680.092670.087810.9980.99392.59260.131

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