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Yorodumi- PDB-3p3d: Crystal structure of the Nup53 RRM domain from Pichia guilliermondii -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p3d | ||||||
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Title | Crystal structure of the Nup53 RRM domain from Pichia guilliermondii | ||||||
Components | Nucleoporin 53 | ||||||
Keywords | NUCLEAR PROTEIN / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / Protein Transport / component of Nuclear Pore Complex / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information structural constituent of nuclear pore / mRNA transport / nuclear pore / protein transport / nuclear membrane / nucleic acid binding Similarity search - Function | ||||||
Biological species | Pichia guilliermondii (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Sampathkumar, P. / Shawn, C. / Bain, K. / Gilmore, J. / Gheyi, T. / Atwell, S. / Thompson, D.A. / Emtage, J.S. / Wasserman, S. / Sauder, J.M. ...Sampathkumar, P. / Shawn, C. / Bain, K. / Gilmore, J. / Gheyi, T. / Atwell, S. / Thompson, D.A. / Emtage, J.S. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the Nup53 RRM domain from Pichia guilliermondii Authors: Sampathkumar, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p3d.cif.gz | 31.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p3d.ent.gz | 19.1 KB | Display | PDB format |
PDBx/mmJSON format | 3p3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p3d_validation.pdf.gz | 425.5 KB | Display | wwPDB validaton report |
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Full document | 3p3d_full_validation.pdf.gz | 425.9 KB | Display | |
Data in XML | 3p3d_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 3p3d_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/3p3d ftp://data.pdbj.org/pub/pdb/validation_reports/p3/3p3d | HTTPS FTP |
-Related structure data
Related structure data | 1wwhS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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: 14517.317 Da / Num. of mol.: 1 / Fragment: RRM Domain residues 261-383 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pichia guilliermondii (fungus) / Gene: NUP53 (gi146415668), PGUG_04532 / Plasmid: BC-pSGX3(BC); modified pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL / References: UniProt: A5DMN1 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.55 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: 100mM sodium acetate, 20% PEG 1500, pH 5.4, 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: Jun 24, 2010 |
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: 2.35→38.62 Å / Num. obs: 5437 / % possible obs: 99.8 % / Redundancy: 21 % / Biso Wilson estimate: 59 Å2 / Rsym value: 0.085 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 21.9 % / Mean I/σ(I) obs: 6.5 / Num. unique all: 782 / Rsym value: 0.406 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Poly-Ala of 1WWH Resolution: 2.35→20.46 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.577 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.353 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 75.06 Å2 / Biso mean: 45.3917 Å2 / Biso min: 29.77 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→20.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.353→2.413 Å / Total num. of bins used: 20
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