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Yorodumi- PDB-2bfx: Mechanism of Aurora-B activation by INCENP and inhibition by Hesp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bfx | ||||||
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Title | Mechanism of Aurora-B activation by INCENP and inhibition by Hesperadin. | ||||||
Components |
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Keywords | TRANSFERASE / KINASE / MITOSIS / INHIBITION / TRANSFERASE COMPLEX | ||||||
Function / homology | Function and homology information meiotic spindle midzone / mitotic cytokinesis checkpoint signaling / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / meiotic spindle midzone assembly / metaphase chromosome alignment / abscission / mitotic spindle midzone assembly / cleavage furrow formation / spindle pole centrosome ...meiotic spindle midzone / mitotic cytokinesis checkpoint signaling / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / meiotic spindle midzone assembly / metaphase chromosome alignment / abscission / mitotic spindle midzone assembly / cleavage furrow formation / spindle pole centrosome / histone H3S10 kinase activity / chromosome passenger complex / protein localization to kinetochore / negative regulation of B cell apoptotic process / positive regulation of cytokinesis / chromosome, centromeric region / mitotic cytokinesis / spindle assembly / spindle midzone / pericentric heterochromatin / post-translational protein modification / chromosome segregation / spindle microtubule / kinetochore / spindle / cellular response to UV / chromosome / midbody / microtubule / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / chromatin / protein kinase binding / negative regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | XENOPUS LAEVIS (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sessa, F. / Mapelli, M. / Ciferri, C. / Tarricone, C. / Areces, L.B. / Schneider, T.R. / Stukenberg, P.T. / Musacchio, A. | ||||||
Citation | Journal: Mol.Cell / Year: 2005 Title: Mechanism of Aurora B Activation by Incenp and Inhibition by Hesperadin Authors: Sessa, F. / Mapelli, M. / Ciferri, C. / Tarricone, C. / Areces, L.B. / Schneider, T.R. / Stukenberg, P.T. / Musacchio, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bfx.cif.gz | 144.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bfx.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 2bfx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/2bfx ftp://data.pdbj.org/pub/pdb/validation_reports/bf/2bfx | HTTPS FTP |
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-Related structure data
Related structure data | 2bfyC 1ol5S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 33537.871 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 78-361 Source method: isolated from a genetically manipulated source Details: PHOSPHORYLATED ON A248 AND B248 / Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q6DE08, non-specific serine/threonine protein kinase #2: Protein/peptide | Mass: 4976.640 Da / Num. of mol.: 2 / Fragment: RESIDUES 798-840 Source method: isolated from a genetically manipulated source Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O13024 #3: 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: 2.3 Å3/Da / Density % sol: 45 % |
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Crystal grow | Details: 0.1M BIS-TRIS PROPANE, 18% PEG3350 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 64766 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.0194 / Mean I/σ(I) obs: 8.4 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OL5 Resolution: 1.8→19.92 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1121828.79 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUN LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.04 Å2 / ksol: 0.369571 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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