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

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Basic information

Entry
Database: PDB / ID: 8ang
TitleStructure of the amyloid-forming peptide LYIQWL from Tc5b, grown from 30% ethanol
ComponentsPeptide LYIQWL from Tc5b
KeywordsPROTEIN FIBRIL / amyloid
Function / homologyETHANOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8812
Polymers8351
Non-polymers461
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: ECD measurements confirmed amyloid formation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint1 kcal/mol
Surface area1150 Å2
Unit cell
Length a, b, c (Å)4.875, 23.713, 40.764
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: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
Has ligand of interestN

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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: 1.41 Å3/Da
Crystal growTemperature: 293 K / Method: evaporation, recrystallization
Details: Peptide was dissolved in 30% ethanol at 0.5 mg/ml concentration, then incubated at 293K overnight.

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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: Jan 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.5→20.5 Å / Num. obs: 895 / % possible obs: 95.01 % / Redundancy: 4.06 % / Biso Wilson estimate: 5.59 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.066 / Net I/σ(I): 13.5
Reflection shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 3.8 / Num. unique obs: 61 / CC1/2: 0.978 / Rrim(I) all: 0.204 / % possible all: 65.59

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrysalisProdata reduction
CrysalisProdata scaling
Fragonphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ideal 5 residue beta strand form the software Fragon

Resolution: 1.5→20.5 Å / SU ML: -0 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 4.4171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.0953 81 9.07 %
Rwork0.0842 812 -
obs0.0852 893 94.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 4.33 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20.5 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms60 0 3 0 63
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00768
X-RAY DIFFRACTIONf_angle_d1.236192
X-RAY DIFFRACTIONf_chiral_restr0.065711
X-RAY DIFFRACTIONf_plane_restr0.00639
X-RAY DIFFRACTIONf_dihedral_angle_d14.158922
LS refinement shellResolution: 1.5→20.5 Å
RfactorNum. reflection% reflection
Rfree0.0953 81 -
Rwork0.0842 812 -
obs--94.8 %

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