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- PDB-8qwv: Structure of the amyloid-forming peptide LYIQNL, grown in the pre... -

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Basic information

Entry
Database: PDB / ID: 8qwv
TitleStructure of the amyloid-forming peptide LYIQNL, grown in the presence of ethanol
ComponentsPeptide LYIQNL
KeywordsPROTEIN FIBRIL / amyloid
Function / homologyETHANOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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

Downloads & links

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Assembly

Deposited unit
A: Peptide LYIQNL
B: Peptide LYIQNL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,6184
Polymers1,5262
Non-polymers922
Water905
1
A: Peptide LYIQNL
B: Peptide LYIQNL
hetero molecules

A: Peptide LYIQNL
B: Peptide LYIQNL
hetero molecules

A: Peptide LYIQNL
B: Peptide LYIQNL
hetero molecules

A: Peptide LYIQNL
B: Peptide LYIQNL
hetero molecules

A: Peptide LYIQNL
B: Peptide LYIQNL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,09020
Polymers7,62910
Non-polymers46110
Water18010
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)4.836, 42.405, 22.262
Angle α, β, γ (deg.)90.000, 94.540, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein/peptide Peptide LYIQNL


Mass: 762.894 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 293 K / Method: evaporation, recrystallization / pH: 4.8
Details: Peptide dissolved in 0.1M acetate (pH 4.80) at 0.15 mg/ml concentration was equilibrated against 60% ethanol

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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: Nov 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.7→19.66 Å / Num. obs: 988 / % possible obs: 99.3 % / Redundancy: 2.83 % / Biso Wilson estimate: 10.67 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.147 / Net I/σ(I): 5.9
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 82 / CC1/2: 0.415 / Rrim(I) all: 0.63 / % possible all: 92.13

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.66 Å / SU ML: 0.1391 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 14.6778
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1893 103 10.49 %
Rwork0.1546 879 -
obs0.1584 982 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.77 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms108 0 6 5 119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041129
X-RAY DIFFRACTIONf_angle_d0.715172
X-RAY DIFFRACTIONf_chiral_restr0.046521
X-RAY DIFFRACTIONf_plane_restr0.002220
X-RAY DIFFRACTIONf_dihedral_angle_d16.450847
LS refinement shellResolution: 1.7→19.66 Å
RfactorNum. reflection% reflection
Rfree0.1893 103 -
Rwork0.1546 879 -
obs--98.69 %
Refinement TLS params.Method: refined / Origin x: 0.62331674088 Å / Origin y: 0.487485497637 Å / Origin z: 6.00345622728 Å
111213212223313233
T0.0192251908832 Å2-0.00995022652758 Å2-0.0127616902705 Å2-0.0801960306386 Å2-0.0200845662974 Å2--0.0883631153349 Å2
L1.49765916043 °2-0.114241025809 °2-0.324242240796 °2-1.49564331004 °20.0606806587372 °2--3.43003534824 °2
S0.0494454859331 Å °-0.155815711794 Å °0.00380062099923 Å °-0.0829569806928 Å °0.00587465277809 Å °-0.0112512077058 Å °0.0719340411263 Å °-0.0722511129361 Å °-0.0566023969725 Å °
Refinement TLS groupSelection details: all

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