+Open data
-Basic information
Entry | Database: PDB / ID: 6qw3 | ||||||
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Title | Calcium-bound gelsolin domain 2 | ||||||
Components | Gelsolin | ||||||
Keywords | STRUCTURAL PROTEIN / amyloidosis / gelsolin / actin-binding | ||||||
Function / homology | Function and homology information striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway ...striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / actin cap / sequestering of actin monomers / regulation of podosome assembly / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / barbed-end actin filament capping / actin polymerization or depolymerization / actin filament depolymerization / cell projection assembly / cardiac muscle cell contraction / podosome / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / phagocytosis, engulfment / cortical actin cytoskeleton / hepatocyte apoptotic process / cilium assembly / sarcoplasm / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / response to muscle stretch / central nervous system development / actin filament organization / protein destabilization / cellular response to type II interferon / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / secretory granule lumen / blood microparticle / ficolin-1-rich granule lumen / amyloid fibril formation / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Scalone, E. / Boni, F. / Milani, M. / Mastrangelo, E. / de Rosa, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2019 Title: High-resolution crystal structure of gelsolin domain 2 in complex with the physiological calcium ion. Authors: Bollati, M. / Scalone, E. / Boni, F. / Mastrangelo, E. / Giorgino, T. / Milani, M. / de Rosa, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qw3.cif.gz | 66.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qw3.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 6qw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/6qw3 ftp://data.pdbj.org/pub/pdb/validation_reports/qw/6qw3 | HTTPS FTP |
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-Related structure data
Related structure data | 1kcqS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13166.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: gelsolin domain 2 (G2) / Source: (gene. exp.) Homo sapiens (human) / Gene: GSN / Production host: Escherichia coli (E. coli) / References: UniProt: P06396 |
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#2: Chemical | ChemComp-CA / |
#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: 1.8 Å3/Da / Density % sol: 31.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 36% PEG5000 MME, 0.1M Sodium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→70.82 Å / Num. obs: 24096 / % possible obs: 99.5 % / Redundancy: 10.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.023 / Rrim(I) all: 0.08 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1103 / CC1/2: 0.579 / Rpim(I) all: 0.409 / Rrim(I) all: 0.874 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KCQ Resolution: 1.3→40.995 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→40.995 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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