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Yorodumi- PDB-2qpm: Leu492Ala mutant of Maize cytokinin oxidase/dehydrogenase complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qpm | |||||||||
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Title | Leu492Ala mutant of Maize cytokinin oxidase/dehydrogenase complexed with benzylurea inhibitor CPBU | |||||||||
Components | Cytokinin dehydrogenase 1 | |||||||||
Keywords | OXIDOREDUCTASE / CYTOKININ OXIDASE/DESHYDROGENASE / FLAVOPROTEIN / FAD / PHENYL-UREA INHIBITOR | |||||||||
Function / homology | Function and homology information cytokinin dehydrogenase / cytokinin dehydrogenase activity / cytokinin metabolic process / FAD binding / oxidoreductase activity / extracellular region Similarity search - Function | |||||||||
Biological species | Zea mays (maize) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Briozzo, P. | |||||||||
Citation | Journal: Biochimie / Year: 2010 Title: Phenyl- and benzylurea cytokinins as competitive inhibitors of cytokinin oxidase/dehydrogenase: a structural study. Authors: Kopecny, D. / Briozzo, P. / Popelkova, H. / Sebela, M. / Koncitikova, R. / Spichal, L. / Nisler, J. / Madzak, C. / Frebort, I. / Laloue, M. / Houba-Herin, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qpm.cif.gz | 123.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qpm.ent.gz | 91.4 KB | Display | PDB format |
PDBx/mmJSON format | 2qpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/2qpm ftp://data.pdbj.org/pub/pdb/validation_reports/qp/2qpm | HTTPS FTP |
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-Related structure data
Related structure data | 2qknC 3kjmC 1w1oS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55315.105 Da / Num. of mol.: 1 / Mutation: L492A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: CKX1 / Variant: Nobilis / Plasmid: pINA6703 / Production host: Yarrowia lipolytica (yeast) / References: UniProt: Q9T0N8, cytokinin dehydrogenase |
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-Sugars , 2 types, 5 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | |
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-Non-polymers , 3 types, 340 molecules
#4: Chemical | ChemComp-FAD / |
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#5: Chemical | ChemComp-246 / |
#6: 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: 2.81 Å3/Da / Density % sol: 56.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 31% (W/v) PEG 5000, 0.5% (w/v)n-octyl beta-D-glucoside, 0.1 M Tris-HCl , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 17, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→25 Å / Num. all: 50659 / Num. obs: 50659 / % possible obs: 97.6 % / Redundancy: 4.08 % / Rsym value: 0.053 |
Reflection shell | Resolution: 1.85→1.9 Å / Rsym value: 0.374 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W1O Resolution: 1.85→25 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.85→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.86 Å
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