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- PDB-3m0u: Crystal Structure of the R21D mutant of alpha-spectrin SH3 domain... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3m0u | ||||||
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Title | Crystal Structure of the R21D mutant of alpha-spectrin SH3 domain. Hexagonal crystal obtained in sodium formate at pH 6.5. | ||||||
![]() | Spectrin alpha chain, brain | ||||||
![]() | SIGNALING PROTEIN / SH3-like barrel / Actin capping / Actin-binding / Calmodulin-binding / Cytoskeleton / Phosphoprotein / SH3 domain | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Gavira, J.A. / Camara-Artigas, A. | ||||||
![]() | ![]() Title: Understanding the polymorphic behaviour of a mutant of the alpha-spectrin SH3 domain by means of two 1.1 A structures Authors: Camara-Artigas, A. / Gavira, J.A. / Casares, S. / Garcia-Ruiz, J.M. / Conejero-Lara, F. / Allen, J.P. / Martinez, J. #1: ![]() Title: The effect of a proline residue on the rate of growth and the space group of alpha-spectrin SH3-domain crystals. Authors: Camara-Artigas, A. / Andujar-Sanchez, M. / Ortiz-Salmeron, E. / Cuadri, C. / Casares, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.2 KB | Display | ![]() |
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PDB format | ![]() | 27.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.2 KB | Display | ![]() |
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Full document | ![]() | 436.4 KB | Display | |
Data in XML | ![]() | 5.1 KB | Display | |
Data in CIF | ![]() | 6.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3m0pC ![]() 3m0qC ![]() 3m0rC ![]() 3m0sC ![]() 3m0tC ![]() 1shgS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 7187.138 Da / Num. of mol.: 1 / Fragment: UNP residues 965 to 1025 / Mutation: R21D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FMT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.86 % |
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Crystal grow | Temperature: 298 K / Method: batch, under oil / pH: 6.5 Details: 2 M sodium formate, 0.1 M MES pH 6.5, batch, under oil, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CCD ADSC_Q210 / Detector: CCD / Date: Mar 4, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97752 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→37.19 Å / Num. all: 29341 / Num. obs: 27903 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 10.78 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 7.1 / Num. unique all: 2330 / Rsym value: 0.094 / % possible all: 81.9 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1SHG Resolution: 1.1→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.162 / WRfactor Rwork: 0.148 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.929 / SU B: 0.644 / SU ML: 0.014 / SU R Cruickshank DPI: 0.027 / SU Rfree: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.028 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.45 Å2 / Biso mean: 19.748 Å2 / Biso min: 8.31 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.128 Å / Total num. of bins used: 20
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