+Open data
-Basic information
Entry | Database: PDB / ID: 7b19 | ||||||
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Title | Mutant Myosin-II-GGG motor domain | ||||||
Components | Myosin-2 heavy chain,Myosin-2 heavy chain | ||||||
Keywords | MOTOR PROTEIN / myosin / mutation / W-helix / hydrolase | ||||||
Function / homology | Function and homology information calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / RHO GTPases activate PAKs / contractile actin filament bundle assembly ...calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / RHO GTPases activate PAKs / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / adenyl nucleotide binding / actomyosin contractile ring / hypotonic response / uropod / actin-myosin filament sliding / detection of mechanical stimulus / apical cortex / negative regulation of actin filament polymerization / bleb assembly / actomyosin / myosin filament / filopodium assembly / myosin II complex / early phagosome / microfilament motor activity / cortical actin cytoskeleton organization / cortical actin cytoskeleton / pseudopodium / cleavage furrow / cytoskeletal motor activity / mitotic cytokinesis / response to mechanical stimulus / response to cAMP / extracellular matrix / 14-3-3 protein binding / cell motility / response to hydrogen peroxide / protein localization / chemotaxis / actin filament binding / cell cortex / regulation of cell shape / cytoplasmic vesicle / cytoskeleton / calmodulin binding / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Ewert, W. / Preller, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Int J Mol Sci / Year: 2020 Title: Unraveling a Force-Generating Allosteric Pathway of Actomyosin Communication Associated with ADP and P i Release. Authors: Franz, P. / Ewert, W. / Preller, M. / Tsiavaliaris, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b19.cif.gz | 318.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b19.ent.gz | 235.9 KB | Display | PDB format |
PDBx/mmJSON format | 7b19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/7b19 ftp://data.pdbj.org/pub/pdb/validation_reports/b1/7b19 | HTTPS FTP |
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-Related structure data
Related structure data | 7b1aC 1vomS 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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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 89983.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: mhcA, DDB_G0286355 / Production host: Dictyostelium discoideum (eukaryote) / References: UniProt: P08799 |
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#5: Sugar | ChemComp-GLC / |
-Non-polymers , 6 types, 109 molecules
#2: Chemical | ChemComp-AD9 / | ||||||
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#3: Chemical | ChemComp-MG / | ||||||
#4: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-MLI / #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
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: 2.84 Å3/Da / Density % sol: 56.72 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.24 M sodium malonate, pH8.0, 27% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→44.59 Å / Num. obs: 33626 / % possible obs: 99.55 % / Redundancy: 2 % / Biso Wilson estimate: 40.17 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.77 |
Reflection shell | Resolution: 2.55→2.64 Å / Mean I/σ(I) obs: 2.09 / Num. unique obs: 3315 / CC1/2: 0.844 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VOM Resolution: 2.55→44.59 Å / SU ML: 0.3339 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5983 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→44.59 Å
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Refine LS restraints |
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LS refinement shell |
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