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- PDB-3s1d: Glu381Ser mutant of maize cytokinin oxidase/dehydrogenase complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3s1d | ||||||
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Title | Glu381Ser mutant of maize cytokinin oxidase/dehydrogenase complexed with N6-isopentenyladenosine | ||||||
![]() | 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 | ![]() | 92.5 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 | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 36.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3s1cC ![]() 3s1eC ![]() 3s1fC ![]() 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 / Sugars , 2 types, 4 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 55315.148 Da / Num. of mol.: 1 / Mutation: E381S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#6: Sugar |
-Non-polymers , 5 types, 400 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/ZIR.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZIR.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / | ||||
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#3: Chemical | ChemComp-ZIR / | ||||
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
-Details
Sequence details | SEQUENCE CONFLICT IN UNP ENTRY Q9T0N8 AT THESE POSITIONS |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.05 % |
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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 4 / Detector: CCD / Date: Apr 9, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: not known / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→50 Å / Num. all: 65377 / Num. obs: 64966 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 26.03 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3BW7 Resolution: 1.75→25.62 Å / Cor.coef. Fo:Fc: 0.9469 / Cor.coef. Fo:Fc free: 0.9292 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 30.84 Å2
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Refine analyze | Luzzati coordinate error obs: 0.272 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→25.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.79 Å / Total num. of bins used: 20
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