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Yorodumi- PDB-8ckq: Crystal structure of maize cytokinin oxidase/dehydrogenase 4 (CKO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ckq | |||||||||
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Title | Crystal structure of maize cytokinin oxidase/dehydrogenase 4 (CKO/CKX4) in complex with inhibitor 2-[(3,5-dichlorophenyl)carbamoylamino]benzamide | |||||||||
Components | Cytokinin dehydrogenase 4 | |||||||||
Keywords | FLAVOPROTEIN / Hormone degradation / plant / inhibitor complex | |||||||||
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: 2 Å | |||||||||
Authors | Kopecny, D. / Briozzo, P. / Morera, S. | |||||||||
Funding support | Czech Republic, 2items
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Citation | Journal: To Be Published Title: Cytokinin oxidase/dehydrogenase inhibitors: progress toward a practice Authors: Nisler, J. / Koncitikova, R. / Klimes, P. / Kadlecova, A. / Murvanidze, N. / Kopecny, D. / Werbrouck, S.P.O. / de Diego, N. / Havlicek, L. / Briozzo, P. / Morera, S. / Zalabak, D. / Spichal, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ckq.cif.gz | 109.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ckq.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ckq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/8ckq ftp://data.pdbj.org/pub/pdb/validation_reports/ck/8ckq | HTTPS FTP |
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-Related structure data
Related structure data | 8cj9C 8ck6C 8cktC 8clwC 8cm2C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 58197.684 Da / Num. of mol.: 1 / Mutation: none Source method: isolated from a genetically manipulated source Details: ZmCKO4 / Source: (gene. exp.) Zea mays (maize) / Gene: CKX4 / Production host: Escherichia coli (E. coli) / References: UniProt: E3T1W8, cytokinin dehydrogenase |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-UZX / Mass: 324.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11Cl2N3O2 / Feature type: SUBJECT OF INVESTIGATION |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-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: 55.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 25% MPD in 50 mM HEPES, pH 7.5, 1.4 mM inhibitor and protein at 9.7 mg ml-1 concentration in the starting drop |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.980109 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980109 Å / Relative weight: 1 |
Reflection | Resolution: 2→49.8 Å / Num. obs: 45188 / % possible obs: 99.8 % / Redundancy: 22.2 % / Biso Wilson estimate: 45.89 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.028 / Rrim(I) all: 0.133 / Rsym value: 0.13 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 22.4 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7101 / CC1/2: 0.71 / Rpim(I) all: 0.57 / Rrim(I) all: 2.764 / Rsym value: 2.703 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→49.19 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.14 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.126
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Displacement parameters | Biso mean: 53.69 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2→49.19 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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