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Yorodumi- PDB-1d1c: DICTYOSTELIUM MYOSIN S1DC (MOTOR DOMAIN FRAGMENT) COMPLEXED WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d1c | ||||||
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Title | DICTYOSTELIUM MYOSIN S1DC (MOTOR DOMAIN FRAGMENT) COMPLEXED WITH N-METHYL-O-NITROPHENYL AMINOETHYLDIPHOSPHATE BERYLLIUM TRIFLUORIDE. | ||||||
Components | MYOSIN | ||||||
Keywords | CONTRACTILE PROTEIN / MYOSIN / MOTILITY / ACTIN-BINDING / MOTOR DOMAIN / NANOLOGS | ||||||
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 / Resolution: 2.3 Å | ||||||
Authors | Gulick, A.M. / Bauer, C.B. / Thoden, J.B. / Pate, E. / Yount, R.G. / Rayment, I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: X-ray structures of the Dictyostelium discoideum myosin motor domain with six non-nucleotide analogs. Authors: Gulick, A.M. / Bauer, C.B. / Thoden, J.B. / Pate, E. / Yount, R.G. / Rayment, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d1c.cif.gz | 173.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d1c.ent.gz | 136 KB | Display | PDB format |
PDBx/mmJSON format | 1d1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/1d1c ftp://data.pdbj.org/pub/pdb/validation_reports/d1/1d1c | 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: 86735.109 Da / Num. of mol.: 1 / Fragment: S1DC MOTOR DOMAIN / Mutation: Q760P, R761N Source method: isolated from a genetically manipulated source 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-NMQ / |
#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: 2.93 Å3/Da / Density % sol: 58.02 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 7 Details: 8.3 % PEG 8000 125 MM NACL 3 MM DTT, pH 7.0, MICROBATCH, temperature 4.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.908 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 7, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 42098 / Num. obs: 42098 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.16 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 2 % / Rmerge(I) obs: 0.243 / % possible all: 93 |
Reflection | *PLUS Num. all: 46312 / Num. measured all: 133036 |
Reflection shell | *PLUS % possible obs: 93 % |
-Processing
Software |
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Refinement | Resolution: 2.3→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.013 |