+Open data
-Basic information
Entry | Database: PDB / ID: 7jqt | ||||||
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Title | Abeta 16-36 beta-hairpin mimic with E22K Italian mutation | ||||||
Components | Abeta 16-36 beta-hairpin mimic VAL-ORT-LYS-LEU-VAL-MEA-PHE-ALA-LYS-ORT-ALA-ILE-ILE-GLY-LEU-MET | ||||||
Keywords | DE NOVO PROTEIN / Alzheimer's disease / amyloid / Abeta / oligomer / familial mutant | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Kreutzer, A.G. / McKnelly, K.J. / Nowick, J.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jqt.cif.gz | 21.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jqt.ent.gz | 13.7 KB | Display | PDB format |
PDBx/mmJSON format | 7jqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jqt_validation.pdf.gz | 413.7 KB | Display | wwPDB validaton report |
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Full document | 7jqt_full_validation.pdf.gz | 413.7 KB | Display | |
Data in XML | 7jqt_validation.xml.gz | 3 KB | Display | |
Data in CIF | 7jqt_validation.cif.gz | 3.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/7jqt ftp://data.pdbj.org/pub/pdb/validation_reports/jq/7jqt | HTTPS FTP |
-Related structure data
Related structure data | 7jqrSC 7jqsC 7jquC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 1794.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.1 % |
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Crystal grow | Temperature: 297.15 K / Method: vapor diffusion, hanging drop / Details: sodium thiocyanate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 123.15 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→17.081 Å / Num. obs: 2159 / % possible obs: 97.63 % / Redundancy: 40.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.008785 / Net I/σ(I): 112.71 |
Reflection shell | Resolution: 2.08→2.154 Å / Rmerge(I) obs: 0.008848 / Num. unique obs: 125 / CC1/2: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JQR Resolution: 2.08→17.081 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 122.71 Å2 / Biso mean: 40.4363 Å2 / Biso min: 11.4 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.08→17.081 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 13.0503 Å / Origin y: 58.5613 Å / Origin z: 4.0722 Å
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Refinement TLS group | Selection details: chain 'A' and (resid 1 through 16 ) |