+Open data
-Basic information
Entry | Database: PDB / ID: 5fw9 | ||||||
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Title | Human Spectrin SH3 domain D48G, E7Y, K60Y | ||||||
Components | SPECTRIN ALPHA CHAIN, NON-ERYTHROCYTIC 1 | ||||||
Keywords | STRUCTURAL PROTEIN / SPECTRIN / SPECTRIN SH3 | ||||||
Function / homology | Function and homology information spectrin / actin filament capping / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / Nephrin family interactions / RHOV GTPase cycle / cortical actin cytoskeleton / RHOU GTPase cycle / Caspase-mediated cleavage of cytoskeletal proteins ...spectrin / actin filament capping / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / Nephrin family interactions / RHOV GTPase cycle / cortical actin cytoskeleton / RHOU GTPase cycle / Caspase-mediated cleavage of cytoskeletal proteins / COPI-mediated anterograde transport / NCAM signaling for neurite out-growth / cell projection / structural constituent of cytoskeleton / specific granule lumen / extracellular vesicle / microtubule cytoskeleton / actin filament binding / tertiary granule lumen / cell junction / actin binding / actin cytoskeleton organization / RAF/MAP kinase cascade / calmodulin binding / cadherin binding / intracellular membrane-bounded organelle / calcium ion binding / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Gallego, P. / Navarro, S. / Ventura, S. / Reverter, D. | ||||||
Citation | Journal: To be Published Title: Human Spectrin SH3 Domain D48G, E7Y, K60Y Authors: Navarro, S. / Gallego, P. / Diaz, M. / Ventura, S. / Reverter, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fw9.cif.gz | 24.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fw9.ent.gz | 15.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/5fw9 ftp://data.pdbj.org/pub/pdb/validation_reports/fw/5fw9 | HTTPS FTP |
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-Related structure data
Related structure data | 1bk2S 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: 7239.262 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN, RESIDUES 965-1025 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q13813 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.31 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979493 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979493 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→42.01 Å / Num. obs: 10702 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.5 |
-Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BK2 Resolution: 1.55→32.25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.091 / 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 mean: 22.174 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→32.25 Å
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Refine LS restraints |
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