+Open data
-Basic information
Entry | Database: PDB / ID: 2f2u | ||||||
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Title | crystal structure of the Rho-kinase kinase domain | ||||||
Components | Rho-associated protein kinase 2 | ||||||
Keywords | TRANSFERASE / enzyme-inhibitor complex | ||||||
Function / homology | Function and homology information positive regulation of centrosome duplication / Rho-dependent protein serine/threonine kinase activity / regulation of cell junction assembly / embryonic morphogenesis / actomyosin structure organization / cortical actin cytoskeleton organization / mitotic cytokinesis / Rho protein signal transduction / smooth muscle contraction / regulation of actin cytoskeleton organization ...positive regulation of centrosome duplication / Rho-dependent protein serine/threonine kinase activity / regulation of cell junction assembly / embryonic morphogenesis / actomyosin structure organization / cortical actin cytoskeleton organization / mitotic cytokinesis / Rho protein signal transduction / smooth muscle contraction / regulation of actin cytoskeleton organization / regulation of circadian rhythm / small GTPase binding / rhythmic process / actin cytoskeleton organization / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Yamaguchi, H. / Hakoshima, T. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Molecular mechanism for the regulation of rho-kinase by dimerization and its inhibition by fasudil Authors: Yamaguchi, H. / Kasa, M. / Amano, M. / Kaibuchi, K. / Hakoshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f2u.cif.gz | 168.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f2u.ent.gz | 133.1 KB | Display | PDB format |
PDBx/mmJSON format | 2f2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/2f2u ftp://data.pdbj.org/pub/pdb/validation_reports/f2/2f2u | HTTPS FTP |
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-Related structure data
Related structure data | 1apmS 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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Details | The second part of the biological assembly for chain A is generated by the two fold axis: y-1, x+1, -z+1 / The second part of the biological assembly for chain B is generated by the two fold axis: y, x, -z+1 |
-Components
#1: Protein | Mass: 45776.020 Da / Num. of mol.: 2 / Fragment: protein kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: ROCK2 / Plasmid: pFastBac-HTa / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q28021, EC: 2.7.1.37 #2: Chemical | #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: 3.76 Å3/Da / Density % sol: 67.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.8M Sodium Citrate, 0.1M Sodium Citrate Buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Apr 20, 2003 Details: a double-crystal monochromator and a horizontal focusing mirror |
Radiation | Monochromator: a double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 53814 / Num. obs: 52492 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.075 |
Reflection shell | Resolution: 2.4→2.49 Å / Rsym value: 0.347 / % possible all: 81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1APM Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.404 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.398→2.459 Å / Total num. of bins used: 20
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