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Yorodumi- PDB-4u5x: Structure of plant small GTPase OsRac1 complexed with the non-hyd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u5x | ||||||
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Title | Structure of plant small GTPase OsRac1 complexed with the non-hydrolyzable GTP analog GMPPNP | ||||||
Components | Rac-like GTP-binding protein 1 | ||||||
Keywords | GTP-BINDING PROTEIN / Small GTPase / Rac / Plant | ||||||
Function / homology | Function and homology information cortical cytoskeleton organization / small GTPase-mediated signal transduction / cell projection / regulation of actin cytoskeleton organization / actin filament organization / defense response / cell cortex / regulation of cell shape / cytoplasmic vesicle / actin cytoskeleton organization ...cortical cytoskeleton organization / small GTPase-mediated signal transduction / cell projection / regulation of actin cytoskeleton organization / actin filament organization / defense response / cell cortex / regulation of cell shape / cytoplasmic vesicle / actin cytoskeleton organization / cytoskeleton / intracellular membrane-bounded organelle / GTPase activity / GTP binding / protein kinase binding / enzyme binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Oryza sativa subsp. japonica (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ohki, I. / Kosami, K. / Fujiwara, T. / Nakagawa, A. / Shimamoto, K. / Kojima, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: The Crystal Structure of the Plant Small GTPase OsRac1 Reveals Its Mode of Binding to NADPH Oxidase Authors: Kosami, K. / Ohki, I. / Nagano, M. / Furuita, K. / Sugiki, T. / Kawano, Y. / Kawasaki, T. / Fujiwara, T. / Nakagawa, A. / Shimamoto, K. / Kojima, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u5x.cif.gz | 55.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u5x.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 4u5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u5x_validation.pdf.gz | 768.5 KB | Display | wwPDB validaton report |
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Full document | 4u5x_full_validation.pdf.gz | 770.6 KB | Display | |
Data in XML | 4u5x_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 4u5x_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/4u5x ftp://data.pdbj.org/pub/pdb/validation_reports/u5/4u5x | HTTPS FTP |
-Related structure data
Related structure data | 2j0vS 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: 19687.576 Da / Num. of mol.: 1 / Fragment: UNP residues 8-183 / Mutation: C32S, Q68L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: RAC1, Os01g0229400, LOC_Os01g12900 / Plasmid: pGEX-6P3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9SSX0 | ||
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#2: Chemical | ChemComp-GNP / | ||
#3: Chemical | ChemComp-MG / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG 6000, MES buffer |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 11521 / % possible obs: 99.8 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 7.7 / % possible all: 100 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2J0V Resolution: 1.9→43.54 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.257 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.078 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→43.54 Å
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Refine LS restraints |
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