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Yorodumi- PDB-2dwk: Crystal structure of the RUN domain of mouse Rap2 interacting pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dwk | |||||||||
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Title | Crystal structure of the RUN domain of mouse Rap2 interacting protein x | |||||||||
Components | Protein RUFY3 | |||||||||
Keywords | PROTEIN BINDING / RUN domain / effector / Rap2 / bundle / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
Function / homology | Function and homology information negative regulation of axonogenesis / positive regulation of intracellular protein transport / anchoring junction / regulation of establishment of cell polarity / positive regulation of axonogenesis / regulation of axonogenesis / endomembrane system / positive regulation of axon extension / filopodium / actin filament organization ...negative regulation of axonogenesis / positive regulation of intracellular protein transport / anchoring junction / regulation of establishment of cell polarity / positive regulation of axonogenesis / regulation of axonogenesis / endomembrane system / positive regulation of axon extension / filopodium / actin filament organization / lamellipodium / nervous system development / growth cone / perikaryon / cell differentiation / positive regulation of cell migration / axon / neuronal cell body / dendrite / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | |||||||||
Authors | Kukimoto-Niino, M. / Murayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Crystal Structure of the RUN Domain of the RAP2-interacting Protein x Authors: Kukimoto-Niino, M. / Takagi, T. / Akasaka, R. / Murayama, K. / Uchikubo-Kamo, T. / Terada, T. / Inoue, M. / Watanabe, S. / Tanaka, A. / Hayashizaki, Y. / Kigawa, T. / Shirouzu, M. / Yokoyama, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dwk.cif.gz | 42.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dwk.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 2dwk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/2dwk ftp://data.pdbj.org/pub/pdb/validation_reports/dw/2dwk | HTTPS FTP |
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-Related structure data
Related structure data | 2cxfC 2cxlC 2dwgC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20254.117 Da / Num. of mol.: 1 / Fragment: RUN domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell free protein synthesis / Gene: Rufy3, D5Bwg0860e, Ripx / Plasmid: PK011025-09 / Production host: Cell free synthesis / References: UniProt: Q9D394 |
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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: 2.84 Å3/Da / Density % sol: 56.73 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.05M SODIUM CHLORIDE, 1.4M AMMONIUM SULFATE, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9792, 0.9795, 0.9640 | ||||||||||||
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 27, 2004 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→50 Å / Num. obs: 16483 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 24.5 Å2 / Rsym value: 0.109 / Net I/σ(I): 14.5 | ||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 5.2 / Rsym value: 0.497 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→33.59 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1897785.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.5477 Å2 / ksol: 0.366412 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 38.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→33.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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