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Yorodumi- PDB-3w3u: Crystal structure of Kap121p mutant R349A/Q350A/D353A/E396A/N430K... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w3u | ||||||
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Title | Crystal structure of Kap121p mutant R349A/Q350A/D353A/E396A/N430K/D438A/N477A | ||||||
Components | Importin subunit beta-3 | ||||||
Keywords | PROTEIN TRANSPORT / HEAT repeat / nuclear import | ||||||
Function / homology | Function and homology information regulation of protein desumoylation / nuclear import signal receptor activity / regulation of mitotic nuclear division / nuclear localization sequence binding / mRNA export from nucleus / protein import into nucleus / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Kobayashi, J. / Matsuura, Y. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Structural basis for cell-cycle-dependent nuclear import mediated by the karyopherin Kap121p. Authors: Kobayashi, J. / Matsuura, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w3u.cif.gz | 209 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w3u.ent.gz | 162.4 KB | Display | PDB format |
PDBx/mmJSON format | 3w3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w3u_validation.pdf.gz | 432.3 KB | Display | wwPDB validaton report |
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Full document | 3w3u_full_validation.pdf.gz | 455.7 KB | Display | |
Data in XML | 3w3u_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 3w3u_validation.cif.gz | 49.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/3w3u ftp://data.pdbj.org/pub/pdb/validation_reports/w3/3w3u | HTTPS FTP |
-Related structure data
Related structure data | 3w3tSC 3w3vC 3w3wC 3w3xC 3w3yC 3w3zC 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 | Mass: 119595.180 Da / Num. of mol.: 1 / Mutation: R349A, Q350A, D353A, E396A, N430K, D438A, N477A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PSE1, KAP121, YMR308C, YM9952.10C / Production host: Escherichia coli (E. coli) / References: UniProt: P32337 |
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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: 3.05 Å3/Da / Density % sol: 59.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M HEPES, 10% 2-propanol, 24% PEG 20000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 14, 2011 |
Radiation | Monochromator: rotated-inclined double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→26.55 Å / Num. all: 44098 / Num. obs: 43084 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.6→2.7 Å / % possible all: 84.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3W3T Resolution: 2.6→26.54 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 12.213 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.537 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.719 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→26.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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