+Open data
-Basic information
Entry | Database: PDB / ID: 5jia | |||||||||
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Title | The Crystal Structure Of IUS-SPRY Domain From RanBP10 | |||||||||
Components | Ran-binding protein 10 | |||||||||
Keywords | RAN-BINDING PROTEIN / BETA SANDWICH / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information MET activates RAS signaling / beta-tubulin binding / ubiquitin ligase complex / cytoskeleton organization / guanyl-nucleotide exchange factor activity / microtubule cytoskeleton organization / small GTPase binding / microtubule cytoskeleton / cell surface receptor signaling pathway / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Hong, S.K. / Kim, K.-H. / Kim, E.E. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: J.Mol.Biol. / Year: 2016 Title: Structural Basis for the Interaction between the IUS-SPRY Domain of RanBPM and DDX-4 in Germ Cell Development. Authors: Hong, S.K. / Kim, K.H. / Song, E.J. / Kim, E.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jia.cif.gz | 673.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jia.ent.gz | 555 KB | Display | PDB format |
PDBx/mmJSON format | 5jia.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/5jia ftp://data.pdbj.org/pub/pdb/validation_reports/ji/5jia | HTTPS FTP |
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-Related structure data
Related structure data | 5ji7SC 5ji9C 5jiuC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 23273.049 Da / Num. of mol.: 16 / Fragment: IUS-SPRY DOMAIN, UNP RESIDUES 29-238 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ranbp10, Kiaa1464 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA(DE3) / References: UniProt: Q6VN19 #2: Chemical | ChemComp-IMD / #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: 2.43 Å3/Da / Density % sol: 49.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.1M BICINE, PH 9.0, 10% PEG 20000, 0- 2% DIOXANE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K PH range: 9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 20, 2010 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 330519 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 14.159 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 2.563 / % possible all: 85.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JI7 Resolution: 1.8→41.25 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.49 / Phase error: 21.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→41.25 Å
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Refine LS restraints |
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LS refinement shell |
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