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- PDB-8anm: Structure of the amyloid-forming peptide LYIQWL from Tc5b, grown ... -

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Basic information

Entry
Database: PDB / ID: 8anm
TitleStructure of the amyloid-forming peptide LYIQWL from Tc5b, grown from water
ComponentsPeptide LYIQWL from Tc5b
KeywordsPROTEIN FIBRIL / amyloid
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsDurvanger, Z.
Funding support Hungary, European Union, 3items
OrganizationGrant numberCountry
Hungarian National Research, Development and Innovation Office2018-1.2.1-NKP-2018-00005 Hungary
European Regional Development FundVEKOP-2.3.2-16-2017-00014, VEKOP-2.3.3-15-2017-00018European Union
Hungarian National Research, Development and Innovation OfficeThematic Excellence Program Synth+ Hungary
CitationJournal: Nat Commun / Year: 2023
Title: Polymorphic amyloid nanostructures of hormone peptides involved in glucose homeostasis display reversible amyloid formation.
Authors: Horvath, D. / Durvanger, Z. / K Menyhard, D. / Sulyok-Eiler, M. / Bencs, F. / Gyulai, G. / Horvath, P. / Taricska, N. / Perczel, A.
History
DepositionAug 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide LYIQWL from Tc5b


Theoretical massNumber of molelcules
Total (without water)8351
Polymers8351
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: ECD measurements confirmed amyloid formation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)9.492, 21.675, 23.686
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein/peptide Peptide LYIQWL from Tc5b


Mass: 835.001 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.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 1.46 Å3/Da / Density % sol: 15.7 %
Crystal growTemperature: 310 K / Method: evaporation, recrystallization
Details: Peptide was dissolved in water in 0.15 mg/ml concentration followed by pH adjustment with NaOH to pH 4.0 - 6.0. Crystals grew after incubation at 310K.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Oct 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 0.9→15.99 Å / Num. obs: 3952 / % possible obs: 99.92 % / Redundancy: 5.57 % / Biso Wilson estimate: 5.24 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.128 / Net I/σ(I): 9.1
Reflection shellResolution: 0.9→0.93 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 392 / CC1/2: 0.761 / Rrim(I) all: 0.672

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
CrysalisProdata scaling
Fragonphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ideal 5 residue beta strand form the software Fragon

Resolution: 0.9→15.99 Å / SU ML: 0.0434 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.087
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1451 393 9.98 %
Rwork0.1299 3543 -
obs0.1314 3936 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 5.11 Å2
Refinement stepCycle: LAST / Resolution: 0.9→15.99 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms60 0 0 5 65
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00972
X-RAY DIFFRACTIONf_angle_d1.1546100
X-RAY DIFFRACTIONf_chiral_restr0.110410
X-RAY DIFFRACTIONf_plane_restr0.005512
X-RAY DIFFRACTIONf_dihedral_angle_d7.7459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9-1.030.23291280.22391153X-RAY DIFFRACTION99.53
1.03-1.30.1311280.15141150X-RAY DIFFRACTION99.38
1.3-15.990.12671370.09821240X-RAY DIFFRACTION99.71

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