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Yorodumi- PDB-1w9j: Myosin II Dictyostelium discoideum motor domain S456Y bound with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w9j | ||||||
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Title | Myosin II Dictyostelium discoideum motor domain S456Y bound with MgADP-AlF4 | ||||||
Components | MYOSIN II HEAVY CHAINMyosin | ||||||
Keywords | MYOSIN / MOLECULAR MOTOR / ATPASE / MOTOR DOMAIN / MUTANT / MUSCLE CONTRACTION | ||||||
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 / negative regulation of actin filament polymerization / apical cortex / 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 / calmodulin binding / cytoskeleton / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | DICTYOSTELIUM DISCOIDEUM (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Morris, C.A. / Coureux, P.-D. / Wells, A.L. / Houdusse, A. / Sweeney, H.L. | ||||||
Citation | Journal: To be Published Title: Structure-Function Analysis of Myosin II Backdoor Mutants Authors: Morris, C.A. / Coureux, P.-D. / Wells, A.L. / Houdusse, A. / Sweeney, H.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w9j.cif.gz | 168.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w9j.ent.gz | 129.9 KB | Display | PDB format |
PDBx/mmJSON format | 1w9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/1w9j ftp://data.pdbj.org/pub/pdb/validation_reports/w9/1w9j | HTTPS FTP |
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-Related structure data
Related structure data | 1w9iC 1w9kC 1w9lC 1mndS 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 , 1 types, 1 molecules A
#1: Protein | Mass: 87897.344 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 1-755 / Mutation: YES Source method: isolated from a genetically manipulated source Details: MGADP-BEFX / Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P08799, EC: 3.6.4.1 |
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-Non-polymers , 5 types, 397 molecules
#2: Chemical | ChemComp-MG / | ||
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#3: Chemical | ChemComp-ADP / | ||
#4: Chemical | ChemComp-ALF / | ||
#5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEERED RESIDUE ASP 2 ASN, CHAIN A ENGINEERED RESIDUE SER 456 TYR, CHAIN A MYOSIN IS A PROTEIN ...ENGINEERED |
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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: 3.1 Å3/Da / Density % sol: 59.4 % |
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Crystal grow | pH: 7 Details: 12% PEG 8000, 50 MM HEPES PH 7, 100 MM NACL, 2 MM DTT, 2 MM NAN3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9793 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 24, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2→76.7 Å / Num. obs: 63165 / % possible obs: 89.4 % / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.98→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.9 / % possible all: 44.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MND Resolution: 2→76.7 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.04 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.25 Å2
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Refinement step | Cycle: LAST / Resolution: 2→76.7 Å
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