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- PDB-8qwu: Structure of the amyloid-forming peptide LYIQNL, grown without ethanol -

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Basic information

Entry
Database: PDB / ID: 8qwu
TitleStructure of the amyloid-forming peptide LYIQNL, grown without ethanol
ComponentsPeptide LYIQNL
KeywordsPROTEIN FIBRIL / amyloid
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 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: Commun Biol / Year: 2024
Title: Solvent induced amyloid polymorphism and the uncovering of the elusive class 3 amyloid topology.
Authors: Durvanger, Z. / Bencs, F. / Menyhard, D.K. / Horvath, D. / Perczel, A.
History
DepositionOct 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide LYIQNL


Theoretical massNumber of molelcules
Total (without water)7631
Polymers7631
Non-polymers00
Water00
1
A: Peptide LYIQNL

A: Peptide LYIQNL

A: Peptide LYIQNL

A: Peptide LYIQNL

A: Peptide LYIQNL


Theoretical massNumber of molelcules
Total (without water)3,8145
Polymers3,8145
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_355x-2,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
Unit cell
Length a, b, c (Å)4.848, 20.005, 42.650
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 LYIQNL


Mass: 762.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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

Crystal growTemperature: 310 K / Method: evaporation, recrystallization / pH: 4.8
Details: the peptide was dissolved in 0.1M acetate buffer, pH 4.80 at 0.12 mg/mL concentration and incubated 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: Jun 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.55→18.11 Å / Num. obs: 706 / % possible obs: 94.01 % / Redundancy: 4.83 % / Biso Wilson estimate: 8.19 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.16 / Net I/σ(I): 7.4
Reflection shellResolution: 1.55→1.61 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 53 / CC1/2: 0.92 / Rrim(I) all: 0.414 / % possible all: 68.83

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
CrysalisProdata scaling
Fragonphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→18.11 Å / SU ML: 0.183 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 16.7572
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2437 70 9.94 %
Rwork0.2344 634 -
obs0.2352 704 93.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.13 Å2
Refinement stepCycle: LAST / Resolution: 1.55→18.11 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms51 0 0 0 51
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012751
X-RAY DIFFRACTIONf_angle_d1.034469
X-RAY DIFFRACTIONf_chiral_restr0.06438
X-RAY DIFFRACTIONf_plane_restr0.00569
X-RAY DIFFRACTIONf_dihedral_angle_d16.24418
LS refinement shellResolution: 1.55→18.11 Å
RfactorNum. reflection% reflection
Rfree0.2437 70 -
Rwork0.2344 634 -
obs--93.74 %

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