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Yorodumi- PDB-2y8f: Structure of the Ran-binding domain from human RanBP3 (wild type) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y8f | ||||||
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Title | Structure of the Ran-binding domain from human RanBP3 (wild type) | ||||||
Components | RAN-BINDING PROTEIN 3 | ||||||
Keywords | PROTEIN TRANSPORT / CRM1-MEDIATED NUCLEAR EXPORT | ||||||
Function / homology | Function and homology information R-SMAD binding / nuclear pore / protein export from nucleus / small GTPase binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Langer, K. / Dian, C. / Rybin, V. / Muller, C.W. / Petosa, C. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Insights Into the Function of the Crm1 Cofactor Ranbp3 from the Structure of its Ran-Binding Domain Authors: Langer, K. / Dian, C. / Rybin, V. / Muller, C.W. / Petosa, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y8f.cif.gz | 203.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y8f.ent.gz | 164 KB | Display | PDB format |
PDBx/mmJSON format | 2y8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/2y8f ftp://data.pdbj.org/pub/pdb/validation_reports/y8/2y8f | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 15547.807 Da / Num. of mol.: 4 / Fragment: RAN BINDING DOMAIN, RESIDUES 320-454 Source method: isolated from a genetically manipulated source Details: ISOFORM3 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H6Z4 #2: Chemical | ChemComp-CL / | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Sequence details | GAM REMAINING RESIDUES FROM TEV CLEAVAGE SITE | |
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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: 2.53 Å3/Da / Density % sol: 51.34 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 30% PEG 3350, 50 MM TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 10, 2009 / Details: TOROIDAL MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48 Å / Num. obs: 33296 / % possible obs: 100 % / Observed criterion σ(I): 4 / Redundancy: 5.6 % / Biso Wilson estimate: 27.51 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→44.399 Å / SU ML: 0.31 / σ(F): 1.38 / Phase error: 19.95 / 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 / Bsol: 58.181 Å2 / ksol: 0.385 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.72 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→44.399 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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