+Open data
-Basic information
Entry | Database: PDB / ID: 6bdj | ||||||
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Title | Crystal structure of dioxygenase Tetur07g02040 | ||||||
Components | Tetur07g02040 | ||||||
Keywords | METAL BINDING PROTEIN / dioxygenase / two-spotted spider mite / agricultural pest / detoxification | ||||||
Function / homology | Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core / Dioxygenase / : / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / ferric iron binding / : / Intradiol ring-cleavage dioxygenases domain-containing protein Function and homology information | ||||||
Biological species | Tetranychus urticae (two-spotted spider mite) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Daneshian, L. / Schlachter, C.R. / Chruszcz, M. | ||||||
Citation | Journal: Insect Biochem.Mol.Biol. / Year: 2019 Title: Structural and functional characterization of an intradiol ring-cleavage dioxygenase from the polyphagous spider mite herbivore Tetranychus urticae Koch. Authors: Schlachter, C.R. / Daneshian, L. / Amaya, J. / Klapper, V. / Wybouw, N. / Borowski, T. / Van Leeuwen, T. / Grbic, V. / Grbic, M. / Makris, T.M. / Chruszcz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bdj.cif.gz | 175.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bdj.ent.gz | 144.3 KB | Display | PDB format |
PDBx/mmJSON format | 6bdj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bdj_validation.pdf.gz | 438.6 KB | Display | wwPDB validaton report |
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Full document | 6bdj_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 6bdj_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 6bdj_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/6bdj ftp://data.pdbj.org/pub/pdb/validation_reports/bd/6bdj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 27933.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetranychus urticae (two-spotted spider mite) Gene: 107361576 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: T1K8P1 #2: Chemical | #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: 2.06 Å3/Da / Density % sol: 40.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M LiSO4, 0.1 M HEPES pH 7.5, 10%w/v PEG3350, 10 mM catechol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→40 Å / Num. obs: 24133 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.032 / Rrim(I) all: 0.064 / Rsym value: 0.056 / Net I/σ(I): 32 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 929 / CC1/2: 0.963 / Rpim(I) all: 0.16 / Rrim(I) all: 0.3 / Rsym value: 0.252 / % possible all: 72.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→40 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.208 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.448 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→40 Å
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Refine LS restraints |
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