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Yorodumi- PDB-5bpt: Atomic-resolution structures of the APC/C subunits Apc4 and the A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bpt | ||||||
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Title | Atomic-resolution structures of the APC/C subunits Apc4 and the Apc5 N-terminal domain | ||||||
Components | MGC81278 protein | ||||||
Keywords | CELL CYCLE / Apc4 / APC/C / anaphase promoting complex | ||||||
Function / homology | Function and homology information anaphase-promoting complex / anaphase-promoting complex-dependent catabolic process / protein K11-linked ubiquitination / regulation of mitotic metaphase/anaphase transition / cell cycle / cell division Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å | ||||||
Authors | Cronin, N. / Yang, J. / Zhang, Z. / Barford, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2015 Title: Atomic-Resolution Structures of the APC/C Subunits Apc4 and the Apc5 N-Terminal Domain. Authors: Cronin, N.B. / Yang, J. / Zhang, Z. / Kulkarni, K. / Chang, L. / Yamano, H. / Barford, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bpt.cif.gz | 254.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bpt.ent.gz | 213.8 KB | Display | PDB format |
PDBx/mmJSON format | 5bpt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/5bpt ftp://data.pdbj.org/pub/pdb/validation_reports/bp/5bpt | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 85415.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: anapc4, MGC81278 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6NU36 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Apc4 was concentrated to 3.5 mg/ml in a buffer of 20 mM Hepes (pH 8.0), 200 mM NaCl and 2 mM DTT. Initial crystal was obtained by vapour diffusion in setting drop in a buffer containing 0.1 ...Details: Apc4 was concentrated to 3.5 mg/ml in a buffer of 20 mM Hepes (pH 8.0), 200 mM NaCl and 2 mM DTT. Initial crystal was obtained by vapour diffusion in setting drop in a buffer containing 0.1 M sodium citrate 5.0, 8% (w/v) PEG 8K. By seeding with the initial crystals, large crystals were grown in a buffer containing 0.1 M sodium citrate 5.0, 3% (w/v) PEG 8K, 250 mM magnesium acetate, 10 mM Tris.HCl (pH 8.5), 200 mM NDSB-211, 4% (v/v) ethylene glycol and 2 mM DTT. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→29.3 Å / Num. all: 15477 / Num. obs: 15477 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 107.57 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 3.2→3.47 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.6 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.2→48.71 Å / Cor.coef. Fo:Fc: 0.9131 / Cor.coef. Fo:Fc free: 0.8692 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.451
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Displacement parameters | Biso max: 266.66 Å2 / Biso mean: 107.87 Å2 / Biso min: 49.75 Å2
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Refine analyze | Luzzati coordinate error obs: 0.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→48.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.42 Å / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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