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Yorodumi- PDB-1cqm: PROTEIN AGGREGATION AND ALZHEIMER'S DISEASE: CRYSTALLOGRAPHIC ANA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cqm | ||||||
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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 | 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 / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å | ||||||
Authors | Kristensen, O. / Otzen, D.E. / Oliveberg, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / 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 | 1cqm.cif.gz | 53.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cqm.ent.gz | 40 KB | Display | PDB format |
PDBx/mmJSON format | 1cqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cqm_validation.pdf.gz | 435.8 KB | Display | wwPDB validaton report |
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Full document | 1cqm_full_validation.pdf.gz | 438.4 KB | Display | |
Data in XML | 1cqm_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 1cqm_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/1cqm ftp://data.pdbj.org/pub/pdb/validation_reports/cq/1cqm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11914.761 Da / Num. of mol.: 2 / Mutation: E41A, E42I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P23370, UniProt: Q5SLP8*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.18 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 400, SODIUM CITRATE, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 20K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||
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: 1.0158 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 6, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0158 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. all: 25338 / Num. obs: 24926 / % possible obs: 94.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.243 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Resolution: 1.65→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1633216.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.1 Å2 / ksol: 0.482 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.025 / 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 / % reflection Rfree: 3.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.304 / % reflection Rfree: 3.7 % / Rfactor Rwork: 0.296 |