+Open data
-Basic information
Entry | Database: PDB / ID: 4f16 | ||||||
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Title | Crystal Structure of the alpha spectrin SH3 domain at pH 5 | ||||||
Components | Spectrin alpha chain, brain | ||||||
Keywords | STRUCTURAL PROTEIN / SH3-like barrel | ||||||
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: 1.93 Å | ||||||
Authors | Camara-Artigas, A. / Gavira, J.A. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the alpha spectrin SH3 domain at pH 5 Authors: Camara-Artigas, A. / Gavira, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f16.cif.gz | 24.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f16.ent.gz | 14.7 KB | Display | PDB format |
PDBx/mmJSON format | 4f16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/4f16 ftp://data.pdbj.org/pub/pdb/validation_reports/f1/4f16 | HTTPS FTP |
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-Related structure data
Related structure data | 1shgS 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: 7229.244 Da / Num. of mol.: 1 / Fragment: SH3 domain, UNP residues 965-1025 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: 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: 2.41 Å3/Da / Density % sol: 48.89 % |
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Crystal grow | Temperature: 298 K / pH: 5 Details: 0.1M Sodium Acetate, 30% PEG 8000, pH 5, capillary counterdiffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 3, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→20 Å / Num. obs: 5427 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.93→2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.199 / % possible all: 78 |
-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: 1SHG Resolution: 1.93→19.51 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.2 / σ(F): 1.34 / Phase error: 28.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.69 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→19.51 Å
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Refine LS restraints |
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LS refinement shell |
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