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Yorodumi- PDB-2cxl: RUN domain of Rap2 interacting protein x, crystallized in I422 sp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cxl | ||||||
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Title | RUN domain of Rap2 interacting protein x, crystallized in I422 space group | ||||||
Components | rap2 interacting protein x | ||||||
Keywords | PROTEIN BINDING / RUN domain / helix 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 / positive regulation of axon extension / endomembrane system / actin filament organization / filopodium ...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 / positive regulation of axon extension / endomembrane system / actin filament organization / filopodium / lamellipodium / nervous system development / growth cone / perikaryon / cell differentiation / positive regulation of cell migration / axon / neuronal cell body / dendrite / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Kukimoto-Niino, M. / Umehara, T. / 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 | 2cxl.cif.gz | 45 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cxl.ent.gz | 31.5 KB | Display | PDB format |
PDBx/mmJSON format | 2cxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cxl_validation.pdf.gz | 422.2 KB | Display | wwPDB validaton report |
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Full document | 2cxl_full_validation.pdf.gz | 425.6 KB | Display | |
Data in XML | 2cxl_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 2cxl_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/2cxl ftp://data.pdbj.org/pub/pdb/validation_reports/cx/2cxl | HTTPS FTP |
-Related structure data
Related structure data | 2cxfC 2dwgC 2dwkC 1wus C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 21445.293 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 / Plasmid: PX040220-04-MD01 / References: UniProt: Q9D394 |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 7.6 Details: PEG4000, Lithium Sulfate, Tris-HCl, pH 7.6, LIQUID DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97888, 0.97951, 0.97600, 0.98300 | |||||||||||||||
Detector | Detector: CCD / Date: May 16, 2005 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.18→50 Å / Num. obs: 4293 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.0547 % / Rsym value: 0.11 / Net I/σ(I): 15.2776 | |||||||||||||||
Reflection shell | Resolution: 3.18→3.29 Å / Mean I/σ(I) obs: 5.51505 / Rsym value: 0.324 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WUS 1wus Resolution: 3.2→42.1 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 111601.45 / 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: 123.806 Å2 / ksol: 0.407703 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 52.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→42.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.18→3.38 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top |