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- PDB-9n35: Mixture of L-peptide FVGGVV and D-peptide mvggvv forms rippled sheets -

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Basic information

Entry
Database: PDB / ID: 9n35
TitleMixture of L-peptide FVGGVV and D-peptide mvggvv forms rippled sheets
Components
  • FVGGVV
  • MVGGVV
KeywordsPROTEIN FIBRIL / rippled sheet / mixed chirality
Function / homology1,1,1,3,3,3-hexafluoropropan-2-ol / polypeptide(D)
Function and homology information
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)R01 AG070895 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01 AG048120 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01 AG074954 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
DepositionJan 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FVGGVV
B: MVGGVV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8106
Polymers1,1372
Non-polymers6724
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-2 kcal/mol
Surface area1770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)20.920, 11.500, 9.390
Angle α, β, γ (deg.)97.22, 90.77, 94.60
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide FVGGVV


Mass: 576.685 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Polypeptide(D) MVGGVV


Mass: 560.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.96 Å3/Da / Density % sol: 37.36 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 3 / Details: hexafluoroisopropanol, 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: Jun 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.1→11.37 Å / Num. obs: 3263 / % possible obs: 92.7 % / Redundancy: 4.2 % / CC1/2: 0.986 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.15 / Net I/σ(I): 6.46
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.1-1.130.6181820.6280.7291
1.13-1.160.4452340.8650.5191
1.16-1.190.3562050.8770.4081
1.19-1.230.3542140.8860.4021
1.23-1.270.4022370.8620.4561
1.27-1.320.3682050.8890.4191
1.32-1.370.2982140.9010.341
1.37-1.420.3181980.9090.3651
1.42-1.480.2341900.9470.2651
1.48-1.560.211870.9610.2381
1.56-1.640.1881750.9440.2171
1.64-1.740.1771630.9620.2071
1.74-1.860.151560.9620.1741
1.86-2.010.1441370.9460.1671
2.01-2.20.1181340.9730.1361
2.2-2.460.11200.9840.1151
2.46-2.840.1161140.9510.1371
2.84-3.480.093900.9870.1061
3.48-4.920.08700.9860.0891
4.92-11.370.091380.9940.1051

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEVERSION Jun 30, 2024 BUILT=20240723data scaling
XDSVERSION Jun 30, 2024 BUILT=20240723data reduction
SHELXTVERSION 2018/2phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→11.37 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18823 327 10 %RANDOM
Rwork0.16334 ---
obs0.16587 2935 92.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.964 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20.08 Å2-0.37 Å2
2--0.97 Å2-0.02 Å2
3----0.85 Å2
Refinement stepCycle: 1 / Resolution: 1.1→11.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms79 0 40 3 122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.013114
X-RAY DIFFRACTIONr_bond_other_d0.0330.01792
X-RAY DIFFRACTIONr_angle_refined_deg1.9831.609164
X-RAY DIFFRACTIONr_angle_other_deg2.1761.631209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.851510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.802201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg5.635154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0293
X-RAY DIFFRACTIONr_gen_planes_other0.0340.0215
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
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_it0.9110.57946
X-RAY DIFFRACTIONr_mcbond_other0.9140.57846
X-RAY DIFFRACTIONr_mcangle_it0.9240.8754
X-RAY DIFFRACTIONr_mcangle_other0.9190.87455
X-RAY DIFFRACTIONr_scbond_it2.6670.98768
X-RAY DIFFRACTIONr_scbond_other2.7070.98466
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2941.483108
X-RAY DIFFRACTIONr_long_range_B_refined1.67310.76897
X-RAY DIFFRACTIONr_long_range_B_other1.1649.02383
X-RAY DIFFRACTIONr_rigid_bond_restr14.8283206
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.101→1.23 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.174 83 -
Rwork0.203 748 -
obs--83.52 %

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