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Yorodumi- PDB-1qkw: Alpha-spectrin Src Homology 3 domain, N47G mutant in the distal loop. -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qkw | ||||||
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Title | Alpha-spectrin Src Homology 3 domain, N47G mutant in the distal loop. | ||||||
Components | ALPHA II SPECTRIN | ||||||
Keywords | CYTOSKELETON / MEMBRANE / SH3 DOMAIN | ||||||
Function / homology | Function and homology information actin filament capping / costamere / cortical actin cytoskeleton / cell projection / actin filament binding / cell junction / actin cytoskeleton organization / calmodulin binding / calcium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | GALLUS GALLUS (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Vega, M.C. / Martinez, J. / Serrano, L. | ||||||
Citation | Journal: Protein Sci. / Year: 2000 Title: Thermodynamic and structural characterization of Asn and Ala residues in the disallowed II' region of the Ramachandran plot. Authors: Vega, M.C. / Martinez, J.C. / Serrano, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qkw.cif.gz | 25.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qkw.ent.gz | 15 KB | Display | PDB format |
PDBx/mmJSON format | 1qkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/1qkw ftp://data.pdbj.org/pub/pdb/validation_reports/qk/1qkw | HTTPS FTP |
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-Related structure data
Related structure data | 1qkxC 1shgS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 7156.084 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) GALLUS GALLUS (chicken) / Tissue: MUSCLESkeletal muscle / Plasmid: PBR322 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07751 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-GOL / |
#4: 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: 2.47 Å3/Da / Density % sol: 50.22 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: PROTEIN WAS CRYSTALLIZED FROM 1.1 M AMMONIUM SULPHATE, 90MM BIS-TRIS PROPANE, 0.9MM EDTA AND 0.9MM DTT., pH 6.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 3.5 / Method: vapor diffusion, hanging drop / Details: Musacchio, A., (1992) Nature, 359, 851. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.2 |
Detector | Date: Aug 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2→15 Å / Num. obs: 3571 / % possible obs: 85 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.4 |
Reflection shell | Resolution: 2→2.2 Å / % possible all: 75 |
Reflection | *PLUS % possible obs: 75 % / Rmerge(I) obs: 0.037 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SHG Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.228 / Rfactor Rfree: 0.28 / Highest resolution: 2 Å / Num. reflection obs: 5796 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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