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Yorodumi- PDB-3kes: Crystal structure of the autoproteolytic domain from the nuclear ... -
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-Basic information
Entry | Database: PDB / ID: 3kes | ||||||
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Title | Crystal structure of the autoproteolytic domain from the nuclear pore complex component NUP145 from Saccharomyces cerevisiae in the Hexagonal, P61 space group | ||||||
Components | Nucleoporin NUP145 | ||||||
Keywords | PROTEIN TRANSPORT / RNA BINDING PROTEIN / Nuclear pore complex / NUP145 / NUP145-N / yeast / autoproteolysis / protein maturation / post-translational modification / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NYSGXRC / RNA-binding / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information protein localization to nuclear inner membrane / nuclear pore localization / nuclear pore central transport channel / telomere tethering at nuclear periphery / regulation of nucleocytoplasmic transport / nuclear pore outer ring / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / structural constituent of nuclear pore ...protein localization to nuclear inner membrane / nuclear pore localization / nuclear pore central transport channel / telomere tethering at nuclear periphery / regulation of nucleocytoplasmic transport / nuclear pore outer ring / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / structural constituent of nuclear pore / RNA export from nucleus / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / subtelomeric heterochromatin formation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / nuclear pore / protein import into nucleus / double-strand break repair / nuclear membrane / chromosome, telomeric region / hydrolase activity / positive regulation of DNA-templated transcription / RNA binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Sampathkumar, P. / Ozyurt, S.A. / Do, J. / Bain, K. / Dickey, M. / Gheyi, T. / Sali, A. / Kim, S.J. / Phillips, J. / Pieper, U. ...Sampathkumar, P. / Ozyurt, S.A. / Do, J. / Bain, K. / Dickey, M. / Gheyi, T. / Sali, A. / Kim, S.J. / Phillips, J. / Pieper, U. / Fernandez-Martinez, J. / Franke, J.D. / Atwell, S. / Thompson, D.A. / Emtage, J.S. / Wasserman, S. / Rout, M. / Sauder, J.M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Proteins / Year: 2010 Title: Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup145. Authors: Sampathkumar, P. / Ozyurt, S.A. / Do, J. / Bain, K.T. / Dickey, M. / Rodgers, L.A. / Gheyi, T. / Sali, A. / Kim, S.J. / Phillips, J. / Pieper, U. / Fernandez-Martinez, J. / Franke, J.D. / ...Authors: Sampathkumar, P. / Ozyurt, S.A. / Do, J. / Bain, K.T. / Dickey, M. / Rodgers, L.A. / Gheyi, T. / Sali, A. / Kim, S.J. / Phillips, J. / Pieper, U. / Fernandez-Martinez, J. / Franke, J.D. / Martel, A. / Tsuruta, H. / Atwell, S. / Thompson, D.A. / Emtage, J.S. / Wasserman, S.R. / Rout, M.P. / Sauder, J.M. / Burley, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kes.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kes.ent.gz | 61 KB | Display | PDB format |
PDBx/mmJSON format | 3kes.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/3kes ftp://data.pdbj.org/pub/pdb/validation_reports/ke/3kes | HTTPS FTP |
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-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: 20409.430 Da / Num. of mol.: 2 / Fragment: residues 442 to 605 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NUP145, RAT10, YGL092W / Plasmid: BC-pSGX3(BC); modified pET26b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Codon+RIL References: UniProt: P49687, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Chemical | ChemComp-EDO / #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: 3.62 Å3/Da / Density % sol: 66.04 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 1600mM tri-sodium citrate dehydrate, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Aug 2, 2009 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25.92 Å / Num. obs: 34126 / % possible obs: 99.2 % / Redundancy: 21.7 % / Biso Wilson estimate: 32.4 Å2 / Rsym value: 0.089 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 19.8 % / Mean I/σ(I) obs: 8.2 / Num. unique all: 4940 / Rsym value: 0.502 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→25.52 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.141 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.27 Å2 / Biso mean: 35.223 Å2 / Biso min: 15.38 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→25.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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