+Open data
-Basic information
Entry | Database: PDB / ID: 5vg2 | ||||||
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Title | Intradiol ring-cleavage Dioxygenase from Tetranychus urticae | ||||||
Components | Intradiol ring-cleavage Dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / Tetranychus urticae / Dioxygenase / Catechol / intradiol ring-cleavage | ||||||
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 / CACODYLATE ION / : / 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: 2.46 Å | ||||||
Authors | Schlachter, C. / Klapper, V. / 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 | 5vg2.cif.gz | 338.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vg2.ent.gz | 277.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/5vg2 ftp://data.pdbj.org/pub/pdb/validation_reports/vg/5vg2 | HTTPS FTP |
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-Related structure data
Related structure data | 6bdjC 4iltS 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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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 56 - 259 / Label seq-ID: 9 - 212
NCS ensembles :
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-Components
#1: Protein | Mass: 26313.551 Da / Num. of mol.: 4 / Fragment: UNP residues 48-259 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetranychus urticae (two-spotted spider mite) Production host: Escherichia coli (E. coli) / References: UniProt: T1K8P1 #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-CAC / #4: 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: 2.04 Å3/Da / Density % sol: 39.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 7.5, 15% w/v PEG6000 |
-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 MX-225 / Detector: CCD / Date: Dec 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 30081 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.064 / Rrim(I) all: 0.116 / Rsym value: 0.077 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 3 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2 / Num. unique obs: 1539 / Rpim(I) all: 0.371 / Rrim(I) all: 0.665 / Rsym value: 0.483 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ILT Resolution: 2.46→50.01 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / ESU R: 0.871 / ESU R Free: 0.283 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.706 Å2
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Refinement step | Cycle: 1 / Resolution: 2.46→50.01 Å
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Refine LS restraints |
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