+Open data
-Basic information
Entry | Database: PDB / ID: 4kf7 | ||||||
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Title | Nup188(aa1-1160) from Myceliophthora thermophila | ||||||
Components | Nup188Nucleoporin 188 | ||||||
Keywords | STRUCTURAL PROTEIN / Nucleoporin | ||||||
Function / homology | Function and homology information structural constituent of nuclear pore / nuclear pore / protein transport Similarity search - Function | ||||||
Biological species | Myceliophthora thermophila (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å | ||||||
Authors | Schwartz, T.U. / Andersen, K.R. | ||||||
Citation | Journal: Elife / Year: 2013 Title: Scaffold nucleoporins Nup188 and Nup192 share structural and functional properties with nuclear transport receptors. Authors: Andersen, K.R. / Onischenko, E. / Tang, J.H. / Kumar, P. / Chen, J.Z. / Ulrich, A. / Liphardt, J.T. / Weis, K. / Schwartz, T.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kf7.cif.gz | 442.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kf7.ent.gz | 364.7 KB | Display | PDB format |
PDBx/mmJSON format | 4kf7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/4kf7 ftp://data.pdbj.org/pub/pdb/validation_reports/kf/4kf7 | 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: 128246.492 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-1160) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myceliophthora thermophila (fungus) / Gene: MYCTH_2303581 / Production host: Escherichia coli (E. coli) / References: UniProt: G2QD05 |
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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: 2.83 Å3/Da / Density % sol: 56.49 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES, 4.5-7.0% w/v PEG4000, 150 mM ammonium sulfate, 1 mM DTT, 1.0-2.5% tert-butanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2012 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→66.8 Å / Num. all: 41673 / Num. obs: 41673 / % possible obs: 100 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 1.8 / Redundancy: 4.1 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 31.3 |
Reflection shell | Resolution: 2.65→2.72 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.65→66.759 Å / SU ML: 0.34 / σ(F): 1.8 / Phase error: 24.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→66.759 Å
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Refine LS restraints |
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LS refinement shell |
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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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