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Yorodumi- PDB-1jx2: CRYSTAL STRUCTURE OF THE NUCLEOTIDE-FREE DYNAMIN A GTPASE DOMAIN,... -
+Open data
-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 | ||||||
Components | Myosin-2 heavy chain,Dynamin-A | ||||||
Keywords | HYDROLASE / dynamin / GTPase / myosin / fusion-protein / Dictyostelium | ||||||
Function / homology | Function and homology information protein processing in phagocytic vesicle / Apoptotic execution phase / sorocarp morphogenesis / protein localization to cleavage furrow / regulation of post-lysosomal vacuole size / phagosome acidification / pinocytosis / calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction ...protein processing in phagocytic vesicle / Apoptotic execution phase / sorocarp morphogenesis / protein localization to cleavage furrow / regulation of post-lysosomal vacuole size / phagosome acidification / pinocytosis / 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 / profilin binding / endosome organization / negative regulation of actin filament polymerization / apical cortex / bleb assembly / midbody abscission / actomyosin / myosin filament / filopodium assembly / myosin II complex / early phagosome / nucleus organization / microfilament motor activity / cortical actin cytoskeleton organization / establishment or maintenance of cell polarity / cortical actin cytoskeleton / intercellular bridge / intracellular distribution of mitochondria / pseudopodium / cleavage furrow / cytoskeletal motor activity / mitotic cytokinesis / phagocytic vesicle / phagocytosis / response to mechanical stimulus / response to cAMP / mitochondrion organization / extracellular matrix / 14-3-3 protein binding / cell motility / actin filament organization / response to bacterium / phospholipid binding / response to hydrogen peroxide / protein localization / chemotaxis / actin filament binding / cell cortex / regulation of cell shape / cytoplasmic vesicle / microtubule binding / microtubule / cytoskeleton / calmodulin binding / GTPase activity / GTP binding / ATP binding / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Niemann, H.H. / Knetsch, M.L.W. / Scherer, A. / Manstein, D.J. / Kull, F.J. | ||||||
Citation | Journal: EMBO J. / Year: 2001 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jx2.cif.gz | 232.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jx2.ent.gz | 180.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/1jx2 ftp://data.pdbj.org/pub/pdb/validation_reports/jx/1jx2 | HTTPS FTP |
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-Related structure data
Related structure data | 1jwyC 1g8xS 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: 124573.531 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: mhcA, DDB_G0286355, dymA, DDB_G0277849 / Plasmid: pM3 / Production host: Dictyostelium discoideum (eukaryote) / Strain (production host): AX3-Orf+ / References: UniProt: P08799, UniProt: Q94464 |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |