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

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Basic information

Entry
Database: PDB / ID: 7jqu
TitleAbeta 16-36 beta-hairpin mimic with E22G Arctic mutation
ComponentsAbeta 16-36 beta-hairpin mimic VAL-ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLN-ORN-ALA-ILE-ILE-GLY-LEU-MET
KeywordsDE NOVO PROTEIN / Alzheimer's disease / amyloid / Abeta / oligomer / familial mutant
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.611 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
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,3803
Polymers5,3803
Non-polymers00
Water23413
1
A: Abeta 16-36 beta-hairpin mimic VAL-ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLN-ORN-ALA-ILE-ILE-GLY-LEU-MET
B: Abeta 16-36 beta-hairpin mimic VAL-ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLN-ORN-ALA-ILE-ILE-GLY-LEU-MET
C: Abeta 16-36 beta-hairpin mimic VAL-ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLN-ORN-ALA-ILE-ILE-GLY-LEU-MET

A: Abeta 16-36 beta-hairpin mimic VAL-ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLN-ORN-ALA-ILE-ILE-GLY-LEU-MET
B: Abeta 16-36 beta-hairpin mimic VAL-ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLN-ORN-ALA-ILE-ILE-GLY-LEU-MET
C: Abeta 16-36 beta-hairpin mimic VAL-ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLN-ORN-ALA-ILE-ILE-GLY-LEU-MET


Theoretical massNumber of molelcules
Total (without water)10,7606
Polymers10,7606
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_556y,x,-z+11
Buried area4950 Å2
ΔGint-32 kcal/mol
Surface area5390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.341, 67.341, 67.341
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-106-

HOH

21C-104-

HOH

31C-105-

HOH

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Components

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


Mass: 1793.286 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.37 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop / Details: sodium citrate, isopropanol, PEG 4000

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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: Feb 15, 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: 2.611→23.81 Å / Num. obs: 3025 / % possible obs: 99.4 % / Redundancy: 93.3 % / CC1/2: 1 / Rmerge(I) obs: 0.01217 / Net I/σ(I): 23.04
Reflection shellResolution: 2.611→2.705 Å / Rmerge(I) obs: 0.2447 / Num. unique obs: 179 / CC1/2: 0.658

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W4H

5w4h


Resolution: 2.611→23.809 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2811 296 9.79 %
Rwork0.2432 2729 -
obs0.2475 3025 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.05 Å2 / Biso mean: 68.8199 Å2 / Biso min: 21.42 Å2
Refinement stepCycle: final / Resolution: 2.611→23.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms375 0 0 13 388
Biso mean---63.68 -
Num. residues----48
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004381
X-RAY DIFFRACTIONf_angle_d0.797501
X-RAY DIFFRACTIONf_chiral_restr0.05863
X-RAY DIFFRACTIONf_plane_restr0.00257
X-RAY DIFFRACTIONf_dihedral_angle_d24.971249
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.6114-3.28870.32851430.30291363
3.2887-23.8090.2661530.22441366
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.1738-3.741-0.79565.3906-0.88677.4281-0.41930.24830.0190.96090.3992-0.60940.0640.6784-0.3990.74870.1511-0.02610.733-0.05210.517812.442719.883740.2601
25.8589-2.0491-6.08276.81716.038310.2287-0.67790.5544-0.5247-0.70020.55380.73921.3018-1.6461-0.04150.5189-0.0832-0.1170.47930.05390.57345.116212.774533.0653
310.6434-0.9398-0.86949.1551-2.67894.0206-0.31-0.87360.5941-0.17750.16430.6093-1.3402-0.1395-0.19590.5735-0.00380.09920.49830.06930.525913.261820.937427.686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )A1 - 16
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 16 )B1 - 16
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 16 )C1 - 16

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