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Yorodumi- PDB-3s1d: Glu381Ser mutant of maize cytokinin oxidase/dehydrogenase complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s1d | ||||||
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Title | Glu381Ser mutant of maize cytokinin oxidase/dehydrogenase complexed with N6-isopentenyladenosine | ||||||
Components | Cytokinin dehydrogenase 1 | ||||||
Keywords | OXIDOREDUCTASE / FAD BINDING PROTEIN / FLAVOPROTEIN / CYTOKININ OXIDASE/DEHYDROGENASE / CYTOKININ BINDING / GLYCOSYLATION / COVALENT FLAVINATION | ||||||
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: 1.75 Å | ||||||
Authors | Kopecny, D. / Briozzo, P. / Morera, S. | ||||||
Citation | Journal: Febs J. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s1d.cif.gz | 125.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s1d.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 3s1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/3s1d ftp://data.pdbj.org/pub/pdb/validation_reports/s1/3s1d | HTTPS FTP |
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-Related structure data
Related structure data | 3s1cC 3s1eC 3s1fC 4ml8C 4mlaC 4o95C 4oalC 3bw7S S: Starting model for refinement C: citing same article (ref.) |
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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 / Sugars , 2 types, 4 molecules A
#1: Protein | Mass: 55315.148 Da / Num. of mol.: 1 / Mutation: E381S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Strain: cultivar Nobilis / Gene: CKX1 / Plasmid: pINA6703 / Production host: Yarrowia lipolytica (yeast) / Strain (production host): Po1g / References: UniProt: Q9T0N8, cytokinin dehydrogenase |
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#6: Sugar |
-Non-polymers , 5 types, 400 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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