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Yorodumi- PDB-3ppz: Crystal structure of CTR1 kinase domain in complex with staurosporine -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ppz | ||||||
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Title | Crystal structure of CTR1 kinase domain in complex with staurosporine | ||||||
Components | Serine/threonine-protein kinase CTR1 | ||||||
Keywords | TRANSFERASE / Kinase / ATP binding / Phosphorylation | ||||||
Function / homology | Function and homology information regulation of post-embryonic root development / regulation of timing of transition from vegetative to reproductive phase / negative regulation of ethylene-activated signaling pathway / sugar mediated signaling pathway / gibberellin biosynthetic process / response to ethylene / regulation of stem cell division / ethylene-activated signaling pathway / response to sucrose / response to fructose ...regulation of post-embryonic root development / regulation of timing of transition from vegetative to reproductive phase / negative regulation of ethylene-activated signaling pathway / sugar mediated signaling pathway / gibberellin biosynthetic process / response to ethylene / regulation of stem cell division / ethylene-activated signaling pathway / response to sucrose / response to fructose / protein serine/threonine/tyrosine kinase activity / protein autophosphorylation / response to hypoxia / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / ATP binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||
Authors | Mayerhofer, H. / Panneerselvam, S. / Mueller-Dieckmann, J. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2012 Title: Protein kinase domain of CTR1 from Arabidopsis thaliana promotes ethylene receptor cross talk. Authors: Mayerhofer, H. / Panneerselvam, S. / Mueller-Dieckmann, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ppz.cif.gz | 230.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ppz.ent.gz | 186.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ppz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/3ppz ftp://data.pdbj.org/pub/pdb/validation_reports/pp/3ppz | HTTPS FTP |
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-Related structure data
Related structure data | 3p86C 3c4cS 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: 35459.387 Da / Num. of mol.: 2 / Fragment: Kinase domain (UNP RESIDUES 540-821) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g03730, CTR1, F17C15_150 / Plasmid: pETM11/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 cc4 References: UniProt: Q05609, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-STU / | |
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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: 2.87 Å3/Da / Density % sol: 57.21 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M K2SO4, 15% w/v PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 31, 2009 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→47.636 Å / Num. all: 17349 / Num. obs: 17053 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 5.4 % / Num. unique all: 2648 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3C4C Resolution: 2.99→46.2 Å / SU ML: 0.44 / σ(F): 0.04 / 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: 32.896 Å2 / ksol: 0.31 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.99→46.2 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: 6
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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