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Yorodumi- PDB-4oal: Crystal structure of maize cytokinin oxidase/dehydrogenase 4 (ZmC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oal | ||||||
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Title | Crystal structure of maize cytokinin oxidase/dehydrogenase 4 (ZmCKO4) in complex with phenylurea inhibitor CPPU in alternative spacegroup | ||||||
Components | Cytokinin dehydrogenase 4 | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN / CYTOKININ OXIDASE/DEHYDROGENASE / PHENYL-UREA INHIBITOR | ||||||
Function / homology | Function and homology information cytokinin dehydrogenase / cytokinin dehydrogenase activity / cytokinin metabolic process / FAD binding / extracellular region Similarity search - Function | ||||||
Biological species | Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kopecny, D. / Morera, S. / Vigouroux, A. / Koncitikova, R. | ||||||
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 | 4oal.cif.gz | 378.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oal.ent.gz | 305.9 KB | Display | PDB format |
PDBx/mmJSON format | 4oal.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/4oal ftp://data.pdbj.org/pub/pdb/validation_reports/oa/4oal | HTTPS FTP |
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-Related structure data
Related structure data | 3s1cC 3s1dC 3s1eC 3s1fC 4ml8C 4mlaC 4o95SC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 56279.270 Da / Num. of mol.: 2 / Fragment: UNP residues 22-541 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: CKX4, CKX4 (CKO4) / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: E3T1W8, cytokinin dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-DMS / #5: Water | ChemComp-HOH / | |
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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: 2.77 Å3/Da / Density % sol: 55.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0,1M HEPES pH 7,5, 50% MPD, cocrystallized with 3mM CPPU in DMSO and 5% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934 Å | ||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2013 | ||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→27.3 Å / Num. all: 101793 / Num. obs: 101537 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 38 Å2 / Rsym value: 0.13 / Net I/σ(I): 11.44 | ||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4O95 Resolution: 1.9→27.25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9336 / SU R Cruickshank DPI: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 38.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.315 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→27.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -38.3433 Å / Origin y: -27.5956 Å / Origin z: 5.8458 Å
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Refinement TLS group |
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