[English] 日本語
Yorodumi- PDB-3m0u: Crystal Structure of the R21D mutant of alpha-spectrin SH3 domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m0u | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the R21D mutant of alpha-spectrin SH3 domain. Hexagonal crystal obtained in sodium formate at pH 6.5. | ||||||
Components | Spectrin alpha chain, brain | ||||||
Keywords | SIGNALING PROTEIN / SH3-like barrel / Actin capping / Actin-binding / Calmodulin-binding / Cytoskeleton / Phosphoprotein / 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 / molecular replacement / Resolution: 1.1 Å | ||||||
Authors | Gavira, J.A. / Camara-Artigas, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2011 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: Journal: Acta Crystallogr.,Sect.D / Year: 2009 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3m0u.cif.gz | 39.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3m0u.ent.gz | 27.3 KB | Display | PDB format |
PDBx/mmJSON format | 3m0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/3m0u ftp://data.pdbj.org/pub/pdb/validation_reports/m0/3m0u | HTTPS FTP |
---|
-Related structure data
Related structure data | 3m0pC 3m0qC 3m0rC 3m0sC 3m0tC 1shgS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-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.) Gallus gallus (chicken) / Gene: SPTAN1, SPTA2 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07751 |
---|---|
#2: Chemical | ChemComp-FMT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.86 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97752 Å |
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: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.1→1.128 Å / Total num. of bins used: 20
|