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- PDB-8gjc: X-ray crystallographic structure of a beta-hairpin peptide derive... -

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Basic information

Entry
Database: PDB / ID: 8gjc
TitleX-ray crystallographic structure of a beta-hairpin peptide derived from Abeta 17-35. (ORN)LVFFAED(ORN)GAI(N-Me-Ile)GLM
Componentsbeta-hairpin peptide derived from Abeta 17-35
KeywordsDE NOVO PROTEIN / oligomer / tetramer / amyloid / Alzheimer's disease
Function / homologyMETHIONINE / DI(HYDROXYETHYL)ETHER / trifluoroacetic acid
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.431 Å
AuthorsKreutzer, A.G. / Ruttenberg, S.M. / Nowick, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG072587 United States
CitationJournal: Biochemistry / Year: 2024
Title: beta-Hairpin Alignment Alters Oligomer Formation in A beta-Derived Peptides.
Authors: Ruttenberg, S.M. / Kreutzer, A.G. / Truex, N.L. / Nowick, J.S.
History
DepositionMar 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: beta-hairpin peptide derived from Abeta 17-35
B: beta-hairpin peptide derived from Abeta 17-35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9608
Polymers3,2142
Non-polymers7476
Water55831
1
A: beta-hairpin peptide derived from Abeta 17-35
B: beta-hairpin peptide derived from Abeta 17-35
hetero molecules

A: beta-hairpin peptide derived from Abeta 17-35
B: beta-hairpin peptide derived from Abeta 17-35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,92116
Polymers6,4284
Non-polymers1,49312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2800 Å2
ΔGint-23 kcal/mol
Surface area5040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.164, 38.164, 32.054
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-217-

HOH

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Components

#1: Protein/peptide beta-hairpin peptide derived from Abeta 17-35 / (ORN)LVFFAED(ORN)GAI(N-Me-Ile)GLM


Mass: 1606.903 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical ChemComp-TFA / trifluoroacetic acid / Trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2HF3O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: Molecular Dynamics Morpheus solution containing 0.12M ethylene glycols mix, 0.1M Buffer System 3 pH 8.5, and 37.5% v/v precipitant mix 4. Molecular Dynamics ethylene glycols mix consists of ...Details: Molecular Dynamics Morpheus solution containing 0.12M ethylene glycols mix, 0.1M Buffer System 3 pH 8.5, and 37.5% v/v precipitant mix 4. Molecular Dynamics ethylene glycols mix consists of 0.3 M diethylene glycol, 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M penta(ethylene glycol). Molecular Dynamics Buffer System 3 consists of 1 M BICINE and 1 M Trisma Base. Molecular Dynamics precipitant mix 4 consists of 25 % w/v hexylene glycol, 25 % w/v poly(ethylene glycol) 1000, and 25 % w/v poly(ethylene glycol) 3350.

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Data collection

DiffractionMean temperature: 103.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.431→23.01 Å / Num. obs: 9354 / % possible obs: 97.02 % / Redundancy: 16 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09013 / Net I/σ(I): 24.44
Reflection shellResolution: 1.431→1.482 Å / Rmerge(I) obs: 1.775 / Num. unique obs: 384 / CC1/2: 0.25

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W4H

5w4h


Resolution: 1.431→23.01 Å / Cross valid method: FREE R-VALUE / σ(F): 7.36 / Phase error: 20.89 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1807 952 10.18 %
Rwork0.1547 --
obs0.1597 9354 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.431→23.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms226 0 44 31 301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d1.146
X-RAY DIFFRACTIONf_dihedral_angle_d36.08172
X-RAY DIFFRACTIONf_chiral_restr0.0838
X-RAY DIFFRACTIONf_plane_restr0.00543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.431-1.510.51781070.5055994X-RAY DIFFRACTION72
1.51-1.60.37361450.3071228X-RAY DIFFRACTION88
1.6-1.720.22981320.19211241X-RAY DIFFRACTION90
1.72-1.90.16951400.15971229X-RAY DIFFRACTION90
1.9-2.170.1661400.15171241X-RAY DIFFRACTION90
2.17-2.740.18891270.12911253X-RAY DIFFRACTION91
2.74-23.010.13811410.12761236X-RAY DIFFRACTION90

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