+Open data
-Basic information
Entry | Database: PDB / ID: 6elx | ||||||
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Title | Oryza sativa DWARF14 | ||||||
Components | Strigolactone esterase D14 | ||||||
Keywords | HYDROLASE / Strigolactone / strigolactone receptor / D14 / ligand binding | ||||||
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 subsp. japonica (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Andersson, I. / Carlsson, G.H. / Hasse, D. | ||||||
Citation | Journal: J. Exp. Bot. / Year: 2018 Title: The elusive ligand complexes of the DWARF14 strigolactone receptor. Authors: Carlsson, G.H. / Hasse, D. / Cardinale, F. / Prandi, C. / Andersson, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6elx.cif.gz | 135 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6elx.ent.gz | 106.5 KB | Display | PDB format |
PDBx/mmJSON format | 6elx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6elx_validation.pdf.gz | 459.7 KB | Display | wwPDB validaton report |
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Full document | 6elx_full_validation.pdf.gz | 459.9 KB | Display | |
Data in XML | 6elx_validation.xml.gz | 27.3 KB | Display | |
Data in CIF | 6elx_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/6elx ftp://data.pdbj.org/pub/pdb/validation_reports/el/6elx | HTTPS FTP |
-Related structure data
Related structure data | 1womS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 29252.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q10QA5, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-MRD / ( | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-MPD / ( | #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: 2.17 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: HEPES pH 7.0, 2-methylpentandiol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.99188 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Nov 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99188 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→44.61 Å / Num. obs: 107538 / % possible obs: 95.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 12.45 Å2 / Rmerge(I) obs: 0.05099 / Net I/σ(I): 16.15 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.4184 / % possible all: 77.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WOM Resolution: 1.35→44.61 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / Phase error: 17.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→44.61 Å
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Refine LS restraints |
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LS refinement shell |
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