+Open data
-Basic information
Entry | Database: PDB / ID: 3wio | ||||||
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Title | Crystal structure of OSD14 in complex with hydroxy D-ring | ||||||
Components | Probable strigolactone esterase D14 | ||||||
Keywords | HYDROLASE / ALPHA/BETA-HYDROLASE FOLD | ||||||
Function / homology | Function and homology information strigolactone biosynthetic process / secondary shoot formation / Hydrolases; Acting on ester bonds / hydrolase activity / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Xue, Y.-L. / Miyakawa, T. / Hou, F. / Qin, H.-M. / Tanokura, M. | ||||||
Citation | Journal: Nat Commun / Year: 2013 Title: Molecular mechanism of strigolactone perception by DWARF14 Authors: Nakamura, H. / Xue, Y.-L. / Miyakawa, T. / Hou, F. / Qin, H.-M. / Fukui, K. / Shi, X. / Ito, E. / Ito, S. / Park, S.-H. / Miyauchi, Y. / Asano, A. / Totsuka, N. / Ueda, T. / Tanokura, M. / Asami, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wio.cif.gz | 117.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wio.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 3wio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/3wio ftp://data.pdbj.org/pub/pdb/validation_reports/wi/3wio | HTTPS FTP |
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-Related structure data
Related structure data | 3vxkSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30024.361 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 54-318 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: D14, D88, HTD2, LOC_Os03g10620, Os03g0203200 / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q10QA5, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-H3M / ( | #3: 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: 2.11 Å3/Da / Density % sol: 41.78 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 8% PEG 20000, 2% 1,4-DIOXANE, 0.1M HEPES, PH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Mar 30, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 30394 / Redundancy: 7.1 % / Rsym value: 0.086 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 7 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.43 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VXK Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.279 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.01 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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