+Open data
-Basic information
Entry | Database: PDB / ID: 1xip | ||||||
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Title | Crystal Structure of the N-terminal Domain of Nup159 | ||||||
Components | Nucleoporin NUP159 | ||||||
Keywords | TRANSPORT PROTEIN / beta-propeller | ||||||
Function / homology | Function and homology information : / adenyl-nucleotide exchange factor activity / nuclear pore localization / nuclear pore central transport channel / nuclear pore cytoplasmic filaments / structural constituent of nuclear pore / poly(A)+ mRNA export from nucleus / nucleocytoplasmic transport / NLS-bearing protein import into nucleus / ribosomal small subunit export from nucleus ...: / adenyl-nucleotide exchange factor activity / nuclear pore localization / nuclear pore central transport channel / nuclear pore cytoplasmic filaments / structural constituent of nuclear pore / poly(A)+ mRNA export from nucleus / nucleocytoplasmic transport / NLS-bearing protein import into nucleus / ribosomal small subunit export from nucleus / ribosomal large subunit export from nucleus / nuclear pore / protein export from nucleus / transcription corepressor activity / nuclear envelope / nuclear membrane / molecular adaptor activity / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Weirich, C.S. / Erzberger, J.P. / Berger, J.M. / Weis, K. | ||||||
Citation | Journal: Mol.Cell / Year: 2004 Title: The N-Terminal Domain of Nup159 Forms a beta-Propeller that Functions in mRNA Export by Tethering the Helicase Dbp5 to the Nuclear Pore Authors: Weirich, C.S. / Erzberger, J.P. / Berger, J.M. / Weis, K. | ||||||
History |
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Remark 650 | HELIX determination method: author determined | ||||||
Remark 700 | SHEET determination method: author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xip.cif.gz | 81.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xip.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/1xip ftp://data.pdbj.org/pub/pdb/validation_reports/xi/1xip | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43177.852 Da / Num. of mol.: 1 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NUP159 / Plasmid: pSV271 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIL / References: UniProt: P40477 |
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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: 2.28 Å3/Da / Density % sol: 37.2 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG3350, ammonium acetate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9793, 1.10 | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 12, 2003 | |||||||||
Radiation | Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→50 Å / Num. all: 13707 / Num. obs: 13707 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 56.26 Å2 / Rsym value: 0.068 / Net I/σ(I): 17.2 | |||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1955 / Rsym value: 0.352 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.936 / SU B: 13.647 / SU ML: 0.282 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 2.636 / ESU R Free: 0.315 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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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 mean: 32.143 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.502→2.566 Å / Total num. of bins used: 20 /
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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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