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- PDB-1jx2: CRYSTAL STRUCTURE OF THE NUCLEOTIDE-FREE DYNAMIN A GTPASE DOMAIN,... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jx2 | ||||||
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Title | CRYSTAL STRUCTURE OF THE NUCLEOTIDE-FREE DYNAMIN A GTPASE DOMAIN, DETERMINED AS MYOSIN FUSION | ||||||
![]() | Myosin-2 heavy chain,Dynamin-A | ||||||
![]() | HYDROLASE / dynamin / GTPase / myosin / fusion-protein / Dictyostelium | ||||||
Function / homology | ![]() protein processing in phagocytic vesicle / Regulation of Apoptosis / Apoptotic execution phase / sorocarp morphogenesis / regulation of post-lysosomal vacuole size / ISG15 antiviral mechanism / phagosome acidification / protein localization to cleavage furrow / pinocytosis / calcium-dependent ATPase activity ...protein processing in phagocytic vesicle / Regulation of Apoptosis / Apoptotic execution phase / sorocarp morphogenesis / regulation of post-lysosomal vacuole size / ISG15 antiviral mechanism / phagosome acidification / protein localization to cleavage furrow / pinocytosis / calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / 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 / response to differentiation-inducing factor 1 / hypotonic response / uropod / mitotic actomyosin contractile ring / actomyosin contractile ring / peroxisome fission / mitotic actomyosin contractile ring contraction / actin-myosin filament sliding / detection of mechanical stimulus / profilin binding / apical cortex / negative regulation of actin filament polymerization / endosome organization / bleb assembly / midbody abscission / actomyosin / substrate-dependent cell migration, cell extension / myosin filament / filopodium assembly / early phagosome / mitochondrial fission / cortical actin cytoskeleton organization / myosin II complex / establishment or maintenance of cell polarity / cortical actin cytoskeleton / microfilament motor activity / intercellular bridge / intracellular distribution of mitochondria / nucleus organization / pseudopodium / cytoskeletal motor activity / cleavage furrow / mitotic cytokinesis / phagocytosis / response to mechanical stimulus / 14-3-3 protein binding / response to cAMP / phagocytic vesicle / mitochondrion organization / extracellular matrix / muscle contraction / cell motility / actin filament organization / response to bacterium / response to hydrogen peroxide / protein localization / phospholipid binding / peroxisome / chemotaxis / actin filament binding / cell cortex / regulation of cell shape / cytoplasmic vesicle / microtubule binding / microtubule / cytoskeleton / calmodulin binding / GTPase activity / GTP binding / mitochondrion / ATP binding / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Niemann, H.H. / Knetsch, M.L.W. / Scherer, A. / Manstein, D.J. / Kull, F.J. | ||||||
![]() | ![]() Title: Crystal structure of a dynamin GTPase domain in both nucleotide-free and GDP-bound forms. Authors: Niemann, H.H. / Knetsch, M.L. / Scherer, A. / Manstein, D.J. / Kull, F.J. | ||||||
History |
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Remark 999 | SEQUENCE According to the author, Electron density map confirm residue 260 to be SER and residue ...SEQUENCE According to the author, Electron density map confirm residue 260 to be SER and residue 323 to be CYS. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 232.8 KB | Display | ![]() |
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PDB format | ![]() | 180.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 786.2 KB | Display | ![]() |
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Full document | ![]() | 810 KB | Display | |
Data in XML | ![]() | 41.7 KB | Display | |
Data in CIF | ![]() | 60.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jwyC ![]() 1g8xS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 124573.531 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Sugar | ChemComp-BGC / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ADP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.468 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, Tris, potassium chloride, magnesium chloride, glucose, methyl-propane-diol, dithiothreitol, EGTA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Oct 13, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→15 Å / Num. obs: 52742 / % possible obs: 97.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.05 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.98 / Rsym value: 0.215 / % possible all: 94.6 |
Reflection | *PLUS Lowest resolution: 15 Å / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 94.6 % / Rmerge(I) obs: 0.215 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1G8X, MYOSIN II CATALYTIC DOMAIN Resolution: 2.3→14.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 380278.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.3914 Å2 / ksol: 0.366682 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→14.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.298 / % reflection Rfree: 7 % / Rfactor Rwork: 0.223 |