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- PDB-9dz0: FKFGG(DPN)(DGL)(DPN)GG, a cyclic peptide with mixed chirality -

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Basic information

Entry
Database: PDB / ID: 9dz0
TitleFKFGG(DPN)(DGL)(DPN)GG, a cyclic peptide with mixed chirality
ComponentsFKFGG(DPN)(DGL)(DPN)GG
KeywordsPROTEIN FIBRIL / peptide with mixed chirality
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: FKFGG(DPN)(DGL)(DPN)GG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,1712
Polymers1,0931
Non-polymers781
Water23413
1
A: FKFGG(DPN)(DGL)(DPN)GG
hetero molecules

A: FKFGG(DPN)(DGL)(DPN)GG
hetero molecules

A: FKFGG(DPN)(DGL)(DPN)GG
hetero molecules

A: FKFGG(DPN)(DGL)(DPN)GG
hetero molecules

A: FKFGG(DPN)(DGL)(DPN)GG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,85710
Polymers5,4665
Non-polymers3915
Water905
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
crystal symmetry operation1_575x,y+2,z1
Unit cell
Length a, b, c (Å)14.130, 29.320, 9.520
Angle α, β, γ (deg.)90.000, 103.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide FKFGG(DPN)(DGL)(DPN)GG


Mass: 1093.211 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DMS is a solvent molecule. It is not covalently linked to the peptide.
Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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

CrystalDensity Matthews: 1.75 Å3/Da / Density % sol: 29.8 %
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: 0.97933 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→14.66 Å / Num. obs: 2926 / % possible obs: 94.3 % / Redundancy: 9.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.12 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.1-1.130.351560.9720.3791
1.13-1.160.3232080.9830.3471
1.16-1.190.3142060.9830.3341
1.19-1.230.3281830.9810.3471
1.23-1.270.3211930.9810.3391
1.27-1.310.3181900.9850.3371
1.31-1.360.2341950.9960.2471
1.36-1.420.2041620.9960.2161
1.42-1.480.2151680.9860.2261
1.48-1.560.191750.9840.21
1.56-1.640.1491570.9940.1581
1.64-1.740.1321460.9970.141
1.74-1.860.1251390.9920.1331
1.86-2.010.1051300.9960.1111
2.01-2.20.1071200.9920.1141
2.2-2.460.0981120.9970.1031
2.46-2.840.092950.9980.0971
2.84-3.480.089870.9940.0951
3.48-4.920.072700.9950.0761
4.92-14.660.062340.9990.0651

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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→14.66 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.981 / Cross valid method: FREE R-VALUE / ESU R: 0.035 / ESU R Free: 0.03
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.1356 293 10.014 %
Rwork0.1292 2633 -
all0.13 --
obs-2926 94.448 %
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: 11.145 Å2
Baniso -1Baniso -2Baniso -3
1-0.063 Å20 Å20.294 Å2
2--0.956 Å20 Å2
3----1.038 Å2
Refinement stepCycle: LAST / Resolution: 1.1→14.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms78 0 4 13 95
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01285
X-RAY DIFFRACTIONr_bond_other_d0.180.01873
X-RAY DIFFRACTIONr_angle_refined_deg1.9981.694110
X-RAY DIFFRACTIONr_angle_other_deg6.5191.694167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.795510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.653202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg6.74156
X-RAY DIFFRACTIONr_chiral_restr0.0580.26
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.02105
X-RAY DIFFRACTIONr_gen_planes_other0.0080.0231
X-RAY DIFFRACTIONr_nbd_refined0.1720.214
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2410.248
X-RAY DIFFRACTIONr_nbtor_refined0.2270.243
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.2780.233
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0610.22
X-RAY DIFFRACTIONr_nbd_other0.2430.216
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1820.25
X-RAY DIFFRACTIONr_mcbond_it0.5010.57640
X-RAY DIFFRACTIONr_mcbond_other0.4950.57438
X-RAY DIFFRACTIONr_mcangle_it0.6880.87550
X-RAY DIFFRACTIONr_mcangle_other0.6830.87550
X-RAY DIFFRACTIONr_scbond_it1.731.11545
X-RAY DIFFRACTIONr_scbond_other1.7431.17846
X-RAY DIFFRACTIONr_scangle_it2.3471.52360
X-RAY DIFFRACTIONr_scangle_other2.3521.59261
X-RAY DIFFRACTIONr_lrange_it2.8739.42590
X-RAY DIFFRACTIONr_lrange_other1.5189.18989
X-RAY DIFFRACTIONr_rigid_bond_restr4.6043158
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
1.1-1.2290.15750.1496750.1498680.9560.9686.40550.134
1.229-1.4170.145740.1526660.1517700.9630.96396.10390.143
1.417-1.7320.167630.1295710.1326500.9620.97497.53850.129
1.732-2.4330.112510.1174570.1165150.9870.98598.64080.134
2.433-14.660.129300.1212640.1222950.9790.98699.6610.153

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