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Yorodumi- PDB-3t35: Arabidopsis thaliana dynamin-related protein 1A in postfission state -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t35 | ||||||
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Title | Arabidopsis thaliana dynamin-related protein 1A in postfission state | ||||||
Components | Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A | ||||||
Keywords | MOTOR PROTEIN / dynamin-like protein 1A / GTPase / membrane fission | ||||||
Function / homology | Function and homology information cell plate formation involved in plant-type cell wall biogenesis / stigma development / regulation of plant-type cell wall organization or biogenesis / regulation of lipid localization / regulation of phragmoplast microtubule organization / cell plate / response to boron-containing substance / cellular response to boron-containing substance levels / cytokinesis by cell plate formation / trichome branching ...cell plate formation involved in plant-type cell wall biogenesis / stigma development / regulation of plant-type cell wall organization or biogenesis / regulation of lipid localization / regulation of phragmoplast microtubule organization / cell plate / response to boron-containing substance / cellular response to boron-containing substance levels / cytokinesis by cell plate formation / trichome branching / root hair initiation / xylem and phloem pattern formation / phragmoplast / protein histidine kinase binding / embryo development ending in seed dormancy / clathrin-coated endocytic vesicle / plasmodesma / plant-type vacuole / clathrin-dependent endocytosis / regulation of establishment of cell polarity / clathrin-coated vesicle / plastid / clathrin binding / regulation of endocytosis / chloroplast thylakoid membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular protein transport / cell cortex / microtubule / cytoskeleton / GTPase activity / GTP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.592 Å | ||||||
Authors | Yan, L.M. / Ma, Y.Y. / Sun, Y.N. / Lou, Z.Y. | ||||||
Citation | Journal: J Mol Cell Biol / Year: 2011 Title: Structural basis for mechanochemical role of Arabidopsis thaliana dynamin-related protein in membrane fission Authors: Yan, L.M. / Ma, Y.Y. / Sun, Y.N. / Gao, J. / Chen, X. / Liu, J. / Wang, C. / Rao, Z. / Lou, Z.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t35.cif.gz | 286.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t35.ent.gz | 228.6 KB | Display | PDB format |
PDBx/mmJSON format | 3t35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t35_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3t35_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3t35_validation.xml.gz | 75.3 KB | Display | |
Data in CIF | 3t35_validation.cif.gz | 101.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/3t35 ftp://data.pdbj.org/pub/pdb/validation_reports/t3/3t35 | HTTPS FTP |
-Related structure data
Related structure data | 3t34C 2x2eS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39911.703 Da / Num. of mol.: 4 / Fragment: UNP residues 1-325, 579-606 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: P42697 #2: Chemical | ChemComp-GDP / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.82 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 160mM sodium formate, 16%(w/v) polyethylene glycol 3350, 40mM magnesium chloride, 6%(w/v) 2-Propanol, 20mM HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.592→50 Å / Num. obs: 28872 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2X2E Resolution: 3.592→43.323 Å / SU ML: 0.6 / σ(F): 0.05 / Phase error: 26.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.2 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.592→43.323 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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