+Open data
-Basic information
Entry | Database: PDB / ID: 5dxy | ||||||
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Title | Crystal structure of Dbr2 | ||||||
Components | Artemisinic aldehyde Delta(11(13)) reductase | ||||||
Keywords | OXIDOREDUCTASE / Dbr2 | ||||||
Function / homology | Function and homology information artemisinic aldehyde Delta11(13)-reductase / 12-oxophytodienoate reductase activity / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / jasmonic acid biosynthetic process / oxylipin biosynthetic process / peroxisome / FMN binding / cytosol Similarity search - Function | ||||||
Biological species | Artemisia annua (sweet wormwood) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Li, L. / Chen, T.T. / Xu, Y.C. | ||||||
Citation | Journal: to be published Title: The Crystal structure of Dbr2 Authors: Li, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dxy.cif.gz | 97.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dxy.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 5dxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dxy_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5dxy_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5dxy_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 5dxy_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/5dxy ftp://data.pdbj.org/pub/pdb/validation_reports/dx/5dxy | HTTPS FTP |
-Related structure data
Related structure data | 5dxxSC 5dy2C 5dy3C 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
#1: Protein | Mass: 42478.051 Da / Num. of mol.: 1 / Mutation: M27L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Artemisia annua (sweet wormwood) / Gene: DBR2 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codonplus(DE3) RIPL References: UniProt: C5H429, artemisinic aldehyde Delta11(13)-reductase |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-5J8 / [[( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.46 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Bis-Tris, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.77→50 Å / Num. obs: 34967 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 16.19 Å2 / Rmerge(I) obs: 0.066 / Χ2: 2.413 / Net I/av σ(I): 43.009 / Net I/σ(I): 15.7 / Num. measured all: 243177 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DXX Resolution: 1.77→37.382 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 16.55 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.05 Å2 / Biso mean: 17.8274 Å2 / Biso min: 7.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.77→37.382 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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