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- PDB-7jqr: Abeta 16-36 beta-hairpin mimic with E22G Arctic mutation -

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Basic information

Entry
Database: PDB / ID: 7jqr
TitleAbeta 16-36 beta-hairpin mimic with E22G Arctic mutation
ComponentsAbeta 16-36 beta-hairpin mimic VAL-ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLY-ORN-ALA-ILE-ILE-GLY-LEU-MET
KeywordsDE NOVO PROTEIN / Alzheimer's disease / amyloid / Abeta / oligomer / familial mutant
Function / homologyIODIDE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.07 Å
AuthorsKreutzer, A.G. / McKnelly, K.J. / Nowick, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097562 United States
CitationJournal: Biochemistry / Year: 2022
Title: Effects of Familial Alzheimer's Disease Mutations on the Assembly of a beta-Hairpin Peptide Derived from A beta 16-36 .
Authors: McKnelly, K.J. / Kreutzer, A.G. / Howitz, W.J. / Haduong, K. / Yoo, S. / Hart, C. / Nowick, J.S.
History
DepositionAug 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Abeta 16-36 beta-hairpin mimic VAL-ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLY-ORN-ALA-ILE-ILE-GLY-LEU-MET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,1034
Polymers1,7221
Non-polymers3813
Water28816
1
A: Abeta 16-36 beta-hairpin mimic VAL-ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLY-ORN-ALA-ILE-ILE-GLY-LEU-MET
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)12,61824
Polymers10,3336
Non-polymers2,28418
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
crystal symmetry operation13_456y-1/4,x+1/4,-z+5/41
crystal symmetry operation18_545-x+1/4,z-1/4,y+1/41
crystal symmetry operation24_555-z+3/4,-y+3/4,-x+3/41
Buried area4830 Å2
ΔGint-34 kcal/mol
Surface area6050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.219, 47.219, 47.219
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-101-

IOD

21A-102-

IOD

31A-212-

HOH

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Components

#1: Protein/peptide Abeta 16-36 beta-hairpin mimic VAL-ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLY-ORN-ALA-ILE-ILE-GLY-LEU-MET


Mass: 1722.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop / Details: calcium chloride, sodium acetate, isopropanol

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Data collection

DiffractionMean temperature: 123.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 13, 2017
RadiationMonochromator: Cu anode / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.07→19.28 Å / Num. obs: 2070 / % possible obs: 99.37 % / Redundancy: 90.7 % / CC1/2: 1 / Rmerge(I) obs: 0.01235 / Rrim(I) all: 0.01747 / Net I/σ(I): 65.87
Reflection shellResolution: 2.075→2.149 Å / Num. unique obs: 126 / CC1/2: 0.999 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_3908refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.07→19.28 Å / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2541 203 9.81 %
Rwork0.2029 1867 -
obs0.208 2070 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.73 Å2 / Biso mean: 40.8307 Å2 / Biso min: 20.94 Å2
Refinement stepCycle: final / Resolution: 2.07→19.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms120 0 3 16 139
Biso mean--81.87 43.12 -
Num. residues----16
LS refinement shellResolution: 2.075→2.149 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2541 203 -
Rwork0.2381 1867 -
all-2070 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 13.6285 Å / Origin y: 13.1734 Å / Origin z: 27.118 Å
111213212223313233
T0.2413 Å20.0003 Å20.0146 Å2-0.2553 Å2-0.0506 Å2--0.2632 Å2
L7.1898 °21.0568 °2-1.8825 °2-9.0501 °2-4.2409 °2--5.7066 °2
S-0.1453 Å °-0.1334 Å °-0.3466 Å °0.4806 Å °0.1761 Å °-0.2847 Å °0.0287 Å °0.4571 Å °0.0589 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 1 through 16 )

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