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Yorodumi- PDB-1qjh: Protein Aggregation and Alzheimer's Disease: Crystallographic Ana... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qjh | ||||||
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Title | Protein Aggregation and Alzheimer's Disease: Crystallographic Analysis of the Phenomenon. Engineered version of the ribosomal protein S6 used as a stable scaffold to study oligomerization. | ||||||
Components | 30S ribosomal protein S6 | ||||||
Keywords | RIBOSOMAL PROTEIN / ALZHEIMER DISEASE / RIBOSOMAL PROTEIN S6 / OLIGOMERIZATION | ||||||
Function / homology | Function and homology information small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kristensen, O. / Otzen, D.E. / Oliveberg, M. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2000 Title: Designed protein tetramer zipped together with a hydrophobic Alzheimer homology: a structural clue to amyloid assembly. Authors: Otzen, D.E. / Kristensen, O. / Oliveberg, M. #1: Journal: Embo J. / Year: 1994 Title: Crystal Structure of the Ribosomal Protein S6 from Thermus Thermophilus Authors: Lindahl, M. / Svensson, L.A. / Liljas, A. / Sedelnikova, S.E. / Eliseikina, I.A. / Fomenkova, N.P. / Nevskaya, N. / Nikonov, S.V. / Garber, M.B. / Muranova, T.A. / Rykonova, A.I. / Amons, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qjh.cif.gz | 33 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qjh.ent.gz | 21.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qjh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qjh_validation.pdf.gz | 427.6 KB | Display | wwPDB validaton report |
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Full document | 1qjh_full_validation.pdf.gz | 429.1 KB | Display | |
Data in XML | 1qjh_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 1qjh_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/1qjh ftp://data.pdbj.org/pub/pdb/validation_reports/qj/1qjh | HTTPS FTP |
-Related structure data
Related structure data | 1cqmC 1cqnC 1risS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11830.700 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: rpsF, rps6 / Production host: Escherichia coli (E. coli) / References: UniProt: P23370 |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / pH: 8.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.995 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999 / Details: BENDABLE MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.995 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 5041 / % possible obs: 99.8 % / Redundancy: 11.6 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 35 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 11 / Rsym value: 0.226 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RIS Resolution: 2.2→35 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 2132615.58 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.2756 Å2 / ksol: 0.384563 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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