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- PDB-3s1f: Asp169Glu mutant of maize cytokinin oxidase/dehydrogenase complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3s1f | |||||||||
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Title | Asp169Glu mutant of maize cytokinin oxidase/dehydrogenase complexed with N6-isopentenyladenine | |||||||||
![]() | Cytokinin dehydrogenase 1 | |||||||||
![]() | OXIDOREDUCTASE / FAD BINDING PROTEIN / FLAVOPROTEIN / CYTOKININ OXIDASE/DEHYDROGENASE / CYTOKININ BINDING / GLYCOSYLATION / COVALENT FLAVINATION | |||||||||
Function / homology | ![]() cytokinin dehydrogenase / cytokinin dehydrogenase activity / cytokinin metabolic process / FAD binding / oxidoreductase activity / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kopecny, D. / Briozzo, P. / Morera, S. | |||||||||
![]() | ![]() Title: Kinetic and structural investigation of the cytokinin oxidase/dehydrogenase active site. Authors: Kopecny, D. / Koncitikova, R. / Popelka, H. / Briozzo, P. / Vigouroux, A. / Kopecna, M. / Zalabak, D. / Sebela, M. / Skopalova, J. / Frebort, I. / Morera, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.2 KB | Display | ![]() |
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PDB format | ![]() | 91.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 35.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3s1cC ![]() 3s1dC ![]() 3s1eC ![]() 4ml8C ![]() 4mlaC ![]() 4o95C ![]() 4oalC ![]() 3bw7S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55371.207 Da / Num. of mol.: 1 / Mutation: D169E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar |
-Non-polymers , 5 types, 317 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/ZIP.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZIP.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-FAD / | ||
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#4: Chemical | ChemComp-ZIP / | ||
#6: Chemical | ChemComp-PEG / | ||
#7: Chemical | ChemComp-GOL / #8: Water | ChemComp-HOH / | |
-Details
Sequence details | SEQUENCE CONFLICT IN UNP ENTRY Q9T0N8 AT THESE POSITIONS. THE AUTHORS SEQUENCE REFER TO GENE BANK ...SEQUENCE CONFLICT IN UNP ENTRY Q9T0N8 AT THESE POSITIONS. THE AUTHORS SEQUENCE REFER TO GENE BANK NUMBER Y18377. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30% (w/v) PEG 1500, 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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2→35 Å / Num. all: 43645 / Num. obs: 43223 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 27.24 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.64 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3BW7 Resolution: 2→31.19 Å / Cor.coef. Fo:Fc: 0.9477 / Cor.coef. Fo:Fc free: 0.9191 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 29.27 Å2
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Refine analyze | Luzzati coordinate error obs: 0.211 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→31.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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