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Yorodumi- PDB-4rj9: Structure of a plant specific C2 domain protein, OsGAP1 from rice -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rj9 | ||||||
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Title | Structure of a plant specific C2 domain protein, OsGAP1 from rice | ||||||
Components | C2 domain-containing protein-like | ||||||
Keywords | LIGASE / Beta_sandwich / Lipid selectivity / calcium-dependent / phospholipid binding / membrane targeting / Cytosol | ||||||
Function / homology | Function and homology information positive regulation of defense response to bacterium => GO:1900426 / positive regulation of response to salt stress / abscisic acid-activated signaling pathway / response to salt stress / GTPase activator activity / positive regulation of GTPase activity / defense response / response to wounding / lipid binding / nucleus ...positive regulation of defense response to bacterium => GO:1900426 / positive regulation of response to salt stress / abscisic acid-activated signaling pathway / response to salt stress / GTPase activator activity / positive regulation of GTPase activity / defense response / response to wounding / lipid binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Miao, R. / Fong, Y.H. / Wong, K.B. / Lam, H.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Site-directed Mutagenesis Shows the Significance of Interactions with Phospholipids and the G-protein OsYchF1 for the Physiological Functions of the Rice GTPase-activating Protein 1 (OsGAP1). Authors: Yung, Y.L. / Cheung, M.Y. / Miao, R. / Fong, Y.H. / Li, K.P. / Yu, M.H. / Chye, M.L. / Wong, K.B. / Lam, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rj9.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rj9.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 4rj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rj9_validation.pdf.gz | 426.8 KB | Display | wwPDB validaton report |
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Full document | 4rj9_full_validation.pdf.gz | 428.2 KB | Display | |
Data in XML | 4rj9_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 4rj9_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/4rj9 ftp://data.pdbj.org/pub/pdb/validation_reports/rj/4rj9 | HTTPS FTP |
-Related structure data
Related structure data | 2cm6S 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: 18573.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: Os02g0327000, OsGAP1, OSJNBb0042G06.10, OsJ_06508, P0476C12.36 Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6YWF1, DNA ligase (ATP) | ||
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#2: Chemical | #3: 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: 2.53 Å3/Da / Density % sol: 51.47 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.1M Potassium sodium tartrate terrahydrate and 20% w/v PEG3350, pH 8.4-9.1, VAPOR DIFFUSION, SITTING DROP, temperature 289K PH range: 8.4-9.1 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 30, 2011 |
Radiation | Monochromator: graded multilayer monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→30.37 Å / Num. all: 23481 / Num. obs: 23481 / % possible obs: 98.1 % / Observed criterion σ(F): 12.3 / Observed criterion σ(I): 5 / Redundancy: 6.9 % / Rmerge(I) obs: 0.106 / Rsym value: 0.307 |
Reflection shell | Resolution: 1.63→30.37 Å / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CM6 Resolution: 1.63→30.365 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 18.92 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.63→30.365 Å
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Refine LS restraints |
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LS refinement shell |
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