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Yorodumi- PDB-1vom: COMPLEX BETWEEN DICTYOSTELIUM MYOSIN AND MGADP AND VANADATE AT 1.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vom | ||||||
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Title | COMPLEX BETWEEN DICTYOSTELIUM MYOSIN AND MGADP AND VANADATE AT 1.9A RESOLUTION | ||||||
Components | MYOSIN | ||||||
Keywords | MUSCLE PROTEIN / MYOSIN / MOLECULAR MOTOR / TRANSITION-STATE ANALOG | ||||||
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 / Resolution: 1.9 Å | ||||||
Authors | Rayment, I. / Smith, C.A. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: X-ray structure of the magnesium(II).ADP.vanadate complex of the Dictyostelium discoideum myosin motor domain to 1.9 A resolution. Authors: Smith, C.A. / Rayment, I. #1: Journal: Biophys.J. / Year: 1995 Title: Structural Studies of Myosin:Nucleotide Complexes: A Revised Model for the Molecular Basis of Muscle Contraction Authors: Fisher, A.J. / Smith, C.A. / Thoden, J. / Smith, R. / Sutoh, K. / Holden, H.M. / Rayment, I. #2: Journal: Biochemistry / Year: 1995 Title: X-Ray Structures of the Myosin Motor Domain of Dictyostelium Discoideum Complexed with Mgadp.Befx and Mgadp.Alf4- Authors: Fisher, A.J. / Smith, C.A. / Thoden, J.B. / Smith, R. / Sutoh, K. / Holden, H.M. / Rayment, I. #3: Journal: Science / Year: 1993 Title: Three-Dimensional Structure of Myosin Subfragment-1: A Molecular Motor Authors: Rayment, I. / Rypniewski, W.R. / Schmidt-Base, K. / Smith, R. / Tomchick, D.R. / Benning, M.M. / Winkelmann, D.A. / Wesenberg, G. / Holden, H.M. #4: Journal: Biochem.Biophys.Res.Commun. / Year: 1993 Title: Force-Generating Domain of Myosin Motor Authors: Itakura, S. / Yamakawa, H. / Toyoshima, Y.Y. / Ishijima, A. / Kojima, T. / Harada, Y. / Yanagida, T. / Wakabayashi, T. / Sutoh, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vom.cif.gz | 178.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vom.ent.gz | 136.2 KB | Display | PDB format |
PDBx/mmJSON format | 1vom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/1vom ftp://data.pdbj.org/pub/pdb/validation_reports/vo/1vom | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 86749.008 Da / Num. of mol.: 1 / Fragment: TRUNCATED AT RESIDUE 762 Source method: isolated from a genetically manipulated source Details: THIS MOLECULE WAS TRUNCATED TO YIELD A FRAGMENT THAT CRYSTALLIZES READILY Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Production host: Dictyostelium discoideum (eukaryote) / References: UniProt: P08799 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-VO4 / |
#4: Chemical | ChemComp-ADP / |
#5: Water | ChemComp-HOH / |
Compound details | SSBOND THIS LIES BETWEEN TWOFOLD RELATED MOLECULES. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.45 Å3/Da / Density % sol: 77.41 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.08 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Feb 1, 1995 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Num. obs: 75066 / % possible obs: 97 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.028 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. measured all: 393986 |
-Processing
Software |
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Refinement | Resolution: 1.9→30 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor all: 0.194 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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