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Yorodumi- PDB-1w9i: Myosin II Dictyostelium discoideum motor domain S456Y bound with ... -
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-Basic information
Entry | Database: PDB / ID: 1w9i | ||||||
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Title | Myosin II Dictyostelium discoideum motor domain S456Y bound with MgADP-BeFx | ||||||
Components | MYOSIN II HEAVY CHAIN | ||||||
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 / contractile actin filament bundle assembly / cell trailing edge ...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 / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / RHO GTPases activate PAKs / 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 / substrate-dependent cell migration, cell extension / myosin filament / filopodium assembly / early phagosome / myosin II complex / cortical actin cytoskeleton organization / microfilament motor activity / cortical actin cytoskeleton / pseudopodium / cytoskeletal motor activity / cleavage furrow / mitotic cytokinesis / response to mechanical stimulus / 14-3-3 protein binding / response to cAMP / extracellular matrix / cell motility / response to hydrogen peroxide / actin filament binding / chemotaxis / protein localization / regulation of cell shape / cell cortex / cytoplasmic vesicle / calmodulin binding / cytoskeleton / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | DICTYOSTELIUM DISCOIDEUM (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 | 1w9i.cif.gz | 177.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w9i.ent.gz | 137.4 KB | Display | PDB format |
PDBx/mmJSON format | 1w9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w9i_validation.pdf.gz | 761.8 KB | Display | wwPDB validaton report |
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Full document | 1w9i_full_validation.pdf.gz | 770.4 KB | Display | |
Data in XML | 1w9i_validation.xml.gz | 28 KB | Display | |
Data in CIF | 1w9i_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/1w9i ftp://data.pdbj.org/pub/pdb/validation_reports/w9/1w9i | HTTPS FTP |
-Related structure data
Related structure data | 1w9jC 1w9kC 1w9lC 1mmaS C: citing same article (ref.) 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 87881.344 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 1-754 / 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, 752 molecules
#2: Chemical | ChemComp-MG / | ||
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#3: Chemical | ChemComp-ADP / | ||
#4: Chemical | ChemComp-BEF / | ||
#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: 3.2 Å3/Da / Density % sol: 60.8 % |
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Crystal grow | pH: 7 Details: 10% PEG 8000, 50 MM HEPES PH 7.0, 100 MM NACL, 2 MM DTT, 2 MM NAN3 IN THE RESERVOIR AND 7% PEG 8000, 50 MM HEPES PH 7.0, 100 MM NACL, 2 MM DTT, 2 MM NAN3 IN THE DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9767 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 30, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9767 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40 Å / Num. obs: 105022 / % possible obs: 96.1 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.75→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.1 / % possible all: 97.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MMA Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / SU B: 1.639 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.095 / 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: 22.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→40 Å
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