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- PDB-8t82: Racemic mixture of amyloid beta segment 35-MVGGVV-40 forms hetero... -

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Basic information

Entry
Database: PDB / ID: 8t82
TitleRacemic mixture of amyloid beta segment 35-MVGGVV-40 forms heterochiral rippled beta-sheet, includes pentafluoropropionic acid
Componentsamyloid beta segment 35-MVGGVV-40, racemic mixture
KeywordsPROTEIN FIBRIL / Rippled beta sheet / amyloid fibril
Function / homologypentafluoropropanoic acid
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.1 Å
AuthorsSawaya, M.R. / Raskatov, J.A. / Hazari, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG074954 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Racemic Peptides from Amyloid beta and Amylin Form Rippled beta-Sheets Rather Than Pleated beta-Sheets.
Authors: Hazari, A. / Sawaya, M.R. / Sajimon, M. / Vlahakis, N. / Rodriguez, J. / Eisenberg, D. / Raskatov, J.A.
History
DepositionJun 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: 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

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Assembly

Deposited unit
A: amyloid beta segment 35-MVGGVV-40, racemic mixture
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7252
Polymers5611
Non-polymers1641
Water181
1
A: amyloid beta segment 35-MVGGVV-40, racemic mixture
hetero molecules

A: amyloid beta segment 35-MVGGVV-40, racemic mixture
hetero molecules

A: amyloid beta segment 35-MVGGVV-40, racemic mixture
hetero molecules

A: amyloid beta segment 35-MVGGVV-40, racemic mixture
hetero molecules

A: amyloid beta segment 35-MVGGVV-40, racemic mixture
hetero molecules

A: amyloid beta segment 35-MVGGVV-40, racemic mixture
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,34812
Polymers3,3646
Non-polymers9846
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation3_566-x,-y+1,-z+11
crystal symmetry operation3_666-x+1,-y+1,-z+11
crystal symmetry operation3_466-x-1,-y+1,-z+11
Unit cell
Length a, b, c (Å)9.560, 18.570, 20.830
Angle α, β, γ (deg.)90.000, 98.400, 90.000
Int Tables number14
Space group name H-MP121/c1
Space group name Hall-P2ybc
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z+1/2
#3: -x,-y,-z
#4: x,-y-1/2,z-1/2

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Components

#1: Protein/peptide amyloid beta segment 35-MVGGVV-40, racemic mixture


Mass: 560.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-YWK / pentafluoropropanoic acid


Mass: 164.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3HF5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 24.59 % / Description: needle-shaped
Crystal growTemperature: 298 K / Method: batch mode / Details: pentafluoropropionic acid, water

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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→13.79 Å / Num. obs: 2485 / % possible obs: 82.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 47.8 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.107 / Net I/σ(I): 10.26
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.1-1.160.2341550.9770.2581
1.16-1.230.22980.9780.2181
1.23-1.310.1683330.9860.1831
1.31-1.420.153540.9880.1631
1.42-1.560.1263220.990.1361
1.56-1.740.1122810.9940.1211
1.74-2.010.0952460.9950.1031
2.01-2.460.0992210.9960.1071
2.46-3.480.0921770.9950.11
3.48-13.790.079980.9880.0851

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALE20220820data scaling
XDS20220820data reduction
SHELXD2013/2phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→13.79 Å / SU ML: 0.0483 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.0567
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1771 238 9.98 %
Rwork0.1523 2146 -
obs0.1548 2384 83.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 6.57 Å2
Refinement stepCycle: LAST / Resolution: 1.1→13.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38 0 10 1 49
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006946
X-RAY DIFFRACTIONf_angle_d1.359664
X-RAY DIFFRACTIONf_chiral_restr0.09537
X-RAY DIFFRACTIONf_plane_restr0.00567
X-RAY DIFFRACTIONf_dihedral_angle_d14.285314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.390.18841010.1551913X-RAY DIFFRACTION70.37
1.39-13.790.1741370.15151233X-RAY DIFFRACTION96.01

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