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Yorodumi- PDB-3myl: Insights into the Importance of Hydrogen Bonding in the Gamma-Pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3myl | ||||||
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Title | Insights into the Importance of Hydrogen Bonding in the Gamma-Phosphate Binding Pocket of Myosin: Structural and Functional Studies of Ser236 | ||||||
Components | Myosin-2 heavy chain | ||||||
Keywords | STRUCTURAL PROTEIN / S1dc / myosin / S236A | ||||||
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: 2 Å | ||||||
Authors | Frye, J.J. / Klenchin, V.A. / Bagshaw, C.R. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Insights into the importance of hydrogen bonding in the gamma-phosphate binding pocket of myosin: structural and functional studies of serine 236 Authors: Frye, J.J. / Klenchin, V.A. / Bagshaw, C.R. / Rayment, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3myl.cif.gz | 180.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3myl.ent.gz | 139.4 KB | Display | PDB format |
PDBx/mmJSON format | 3myl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3myl_validation.pdf.gz | 446.9 KB | Display | wwPDB validaton report |
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Full document | 3myl_full_validation.pdf.gz | 464.9 KB | Display | |
Data in XML | 3myl_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 3myl_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/3myl ftp://data.pdbj.org/pub/pdb/validation_reports/my/3myl | HTTPS FTP |
-Related structure data
Related structure data | 3myhC 3mykC 1vomS 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
#1: Protein | Mass: 86731.109 Da / Num. of mol.: 1 / Mutation: S236A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: DDB_G0286355, mhcA / Plasmid: pDXA / Production host: Dictyostelium discoideum (eukaryote) / Strain (production host): ORF+ / References: UniProt: P08799 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-POP / |
#4: 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: 2.92 Å3/Da / Density % sol: 57.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 12.5% MePEG5K, 117mM ammonium acetate, 100mM Hepps, 2mM MgCl2, 2mM sodium pyrophosphate , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.00707 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2008 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00707 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 69055 / Num. obs: 69055 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.9 / Num. unique all: 6769 / Rsym value: 0.406 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1VOM Resolution: 2→29.69 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.901 / SU B: 3.323 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R Free: 0.159 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.093 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.998→2.05 Å / Total num. of bins used: 20
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