+Open data
-Basic information
Entry | Database: PDB / ID: 2f2v | ||||||
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Title | alpha-spectrin SH3 domain A56G mutant | ||||||
Components | Spectrin alpha chain, brain | ||||||
Keywords | SIGNALING PROTEIN / Src homology 3 domain spectrin | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Camara-Artigas, A. / Conejero-Lara, F. / Casares, S. / Lopez-Mayorga, O. / Vega, C. | ||||||
Citation | Journal: Proteins / Year: 2007 Title: Cooperative propagation of local stability changes from low-stability and high-stability regions in a SH3 domain Authors: Casares, S. / Lopez-Mayorga, O. / Vega, M.C. / Camara-Artigas, A. / Conejero-Lara, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f2v.cif.gz | 26 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f2v.ent.gz | 16 KB | Display | PDB format |
PDBx/mmJSON format | 2f2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f2v_validation.pdf.gz | 429.5 KB | Display | wwPDB validaton report |
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Full document | 2f2v_full_validation.pdf.gz | 429.9 KB | Display | |
Data in XML | 2f2v_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | 2f2v_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/2f2v ftp://data.pdbj.org/pub/pdb/validation_reports/f2/2f2v | HTTPS FTP |
-Related structure data
Related structure data | 2cdtC 2f2wC 2f2xC 1shgS C: citing same article (ref.) S: Starting model for refinement |
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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: 7215.218 Da / Num. of mol.: 1 / Fragment: Src-homology 3 domain, SH3 domain / Mutation: A56G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: SPTAN1, SPTA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P07751 | ||
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#2: Chemical | #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: 1.586 Å3/Da / Density % sol: 22.46 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2M Sodium Formiate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: BRUKER PROTEUM X8 / Detector: CCD / Date: Oct 5, 2005 / Details: Montel Optics |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→40 Å / Num. all: 4251 / Num. obs: 3983 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.32 % / Rmerge(I) obs: 0.0273 / Rsym value: 0.0266 / Net I/σ(I): 31.37 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 1.17 % / Rmerge(I) obs: 0.0792 / Mean I/σ(I) obs: 11.5 / Num. unique all: 406 / Rsym value: 0.0475 / % possible all: 70.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SHG Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.902 / SU B: 1.971 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3983 / ESU R: 0.201 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.387 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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