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Yorodumi- PDB-6lje: Crystal structure of gelsolin G3 domain (calcium and magnesium co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lje | |||||||||
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Title | Crystal structure of gelsolin G3 domain (calcium and magnesium condition) | |||||||||
Components | Gelsolin | |||||||||
Keywords | CYTOSOLIC PROTEIN / fragmin / gelsolin family protein / calcium regulation / actin filament severing | |||||||||
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 cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding ...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 cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap / regulation of podosome assembly / sequestering of actin monomers / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / barbed-end actin filament capping / cell projection assembly / cardiac muscle cell contraction / podosome / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / cortical actin cytoskeleton / phagocytosis, engulfment / hepatocyte apoptotic process / sarcoplasm / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / 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 / ficolin-1-rich granule lumen / amyloid fibril formation / blood microparticle / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å | |||||||||
Authors | Takeda, S. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: J.Muscle Res.Cell.Motil. / Year: 2020 Title: Novel inter-domain Ca2+-binding site in the gelsolin superfamily protein fragmin. Authors: Takeda, S. / Fujiwara, I. / Sugimoto, Y. / Oda, T. / Narita, A. / Maeda, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lje.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lje.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 6lje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lje_validation.pdf.gz | 435.3 KB | Display | wwPDB validaton report |
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Full document | 6lje_full_validation.pdf.gz | 435.3 KB | Display | |
Data in XML | 6lje_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 6lje_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/6lje ftp://data.pdbj.org/pub/pdb/validation_reports/lj/6lje | HTTPS FTP |
-Related structure data
Related structure data | 6kwzC 6ljcC 6ljdC 6ljfC 3ffkS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11259.854 Da / Num. of mol.: 2 / Fragment: UNP residues 297-397 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSN / Production host: Escherichia coli (E. coli) / References: UniProt: P06396 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 44.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: PEG3350, ammonium sulphate, calcium chloride, magnesium chloride |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→40.751 Å / Num. obs: 37286 / % possible obs: 96.5 % / Redundancy: 5.107 % / Biso Wilson estimate: 24.303 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.058 / Χ2: 1.022 / Net I/σ(I): 15.58 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ffk Resolution: 1.4→40.75 Å / SU ML: 0.1666 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9788
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→40.75 Å
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Refine LS restraints |
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LS refinement shell |
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