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Yorodumi- PDB-3myk: Insights into the Importance of Hydrogen Bonding in the Gamma-Pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3myk | ||||||
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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 / 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: 1.84 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 | 3myk.cif.gz | 167.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3myk.ent.gz | 128.2 KB | Display | PDB format |
PDBx/mmJSON format | 3myk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/3myk ftp://data.pdbj.org/pub/pdb/validation_reports/my/3myk | HTTPS FTP |
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-Related structure data
Related structure data | 3myhC 3mylC 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-BIT / (-)- |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ANP / |
#5: 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: 2.86 Å3/Da / Density % sol: 57.01 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12% PEG8K, 250mM MgCl2, 100mM MOPS, 2mM AMPPNP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.97885 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 20, 2005 / Details: 3.3 Undulator |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97885 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→28.91 Å / Num. all: 84770 / Num. obs: 84770 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 35.7 |
Reflection shell | Resolution: 1.84→1.91 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 5.3 / Num. unique all: 8291 / Rsym value: 0.152 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1VOM Resolution: 1.84→28.91 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.337 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R Free: 0.119 / 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: 26.866 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→28.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.842→1.89 Å / Total num. of bins used: 20
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