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Yorodumi- PDB-1mnd: TRUNCATED HEAD OF MYOSIN FROM DICTYOSTELIUM DISCOIDEUM COMPLEXED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mnd | ||||||
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Title | TRUNCATED HEAD OF MYOSIN FROM DICTYOSTELIUM DISCOIDEUM COMPLEXED WITH MGADP-ALF4 | ||||||
Components | MYOSIN | ||||||
Keywords | CONTRACTILE PROTEIN / ATPASE / MYOSIN / COILED COIL / ACTIN-BINDING / ATP-BINDING / HEPTAD REPEAT PATTERN / METHYLATION / ALKYLATION / PHOSPHORYLATION | ||||||
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: 2.6 Å | ||||||
Authors | Smith, C.A. / Rayment, I. | ||||||
Citation | 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. #1: 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. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mnd.cif.gz | 146.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mnd.ent.gz | 111.5 KB | Display | PDB format |
PDBx/mmJSON format | 1mnd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/1mnd ftp://data.pdbj.org/pub/pdb/validation_reports/mn/1mnd | HTTPS FTP |
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-Related 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: 86749.008 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN / Mutation: Q760L, R761P, I762N Source method: isolated from a genetically manipulated source Details: GENETICALLY TRUNCATED HEAD OF MYOSIN FROM DICTYOSTELIUM DISCOIDEUM, LIGANDS ADP AND ALF(4) Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Production host: Dictyostelium discoideum (eukaryote) / References: UniProt: P08799, EC: 3.6.1.32 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ALF / |
#4: Chemical | ChemComp-ADP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.61 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
Detector | Date: Sep 15, 1994 |
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Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.6 Å / Num. obs: 29506 / % possible obs: 96 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.061 |
-Processing
Software |
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Refinement | Resolution: 2.6→15 Å / Num. reflection obs: 29334 / σ(F): 0 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→15 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.242 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_planar_d / Dev ideal: 0.016 |