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Yorodumi- PDB-3m0r: Crystal Structure of the R21D mutant of alpha-spectrin SH3 domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m0r | ||||||
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Title | Crystal Structure of the R21D mutant of alpha-spectrin SH3 domain. Crystal obtained in ammonium sulphate at pH 6. | ||||||
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 costamere / actin filament capping / 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m0r.cif.gz | 42 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m0r.ent.gz | 28.8 KB | Display | PDB format |
PDBx/mmJSON format | 3m0r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/3m0r ftp://data.pdbj.org/pub/pdb/validation_reports/m0/3m0r | HTTPS FTP |
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-Related structure data
Related structure data | 3m0pC 3m0qC 3m0sC 3m0tC 3m0uC 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: 7187.138 Da / Num. of mol.: 1 / Fragment: SH3 domain (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 |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.48 Å3/Da / Density % sol: 50.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.8 M ammonium sulphate, 0.1 M Bis-Tris pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1.033 Å |
Detector | Type: CCD ADSC_Q210 / Detector: CCD / Date: Apr 4, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→31.799 Å / Num. all: 29563 / Num. obs: 28144 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 36.394 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 6.4 / Num. unique all: 2867 / Rsym value: 0.302 / % possible all: 98.8 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1SHG Resolution: 1.1→18.05 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.198 / WRfactor Rwork: 0.176 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9 / SU B: 0.76 / SU ML: 0.017 / SU R Cruickshank DPI: 0.032 / SU Rfree: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.032 / ESU R Free: 0.033 / 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: 47.49 Å2 / Biso mean: 14.168 Å2 / Biso min: 6.17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→18.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.102→1.13 Å / Total num. of bins used: 20
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