+Open data
-Basic information
Entry | Database: PDB / ID: 3gl2 | ||||||
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Title | Crystal structure of dicamba monooxygenase bound to dicamba | ||||||
Components | DdmC | ||||||
Keywords | OXIDOREDUCTASE / Rieske protein / non-heme mononuclear iron / oxygenase | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen into the other donor / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / : / monooxygenase activity / 2 iron, 2 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | Stenotrophomonas maltophilia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Wilson, M.A. / Dumitru, R. / Jiang, W.Z. / Weeks, D.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Crystal structure of dicamba monooxygenase: a Rieske nonheme oxygenase that catalyzes oxidative demethylation. Authors: Dumitru, R. / Jiang, W.Z. / Weeks, D.P. / Wilson, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gl2.cif.gz | 405 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gl2.ent.gz | 333.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gl2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gl2_validation.pdf.gz | 476.7 KB | Display | wwPDB validaton report |
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Full document | 3gl2_full_validation.pdf.gz | 495.8 KB | Display | |
Data in XML | 3gl2_validation.xml.gz | 42 KB | Display | |
Data in CIF | 3gl2_validation.cif.gz | 59.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/3gl2 ftp://data.pdbj.org/pub/pdb/validation_reports/gl/3gl2 | HTTPS FTP |
-Related structure data
Related structure data | 3gkeSC 3gl0C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 2 - 155 / Label seq-ID: 2 - 155
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-Components
#1: Protein | Mass: 38641.695 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria) Strain: DI-6 / Gene: ddmC / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5S3I3 #2: Chemical | #3: Chemical | #4: Chemical | #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: 2.62 Å3/Da / Density % sol: 53.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 5% PEG 4000, 100 mM sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2007 / Details: Bent Rh coated conical Si mirror |
Radiation | Monochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→36 Å / Num. all: 68055 / Num. obs: 67158 / % possible obs: 98.41 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.5 / Num. unique all: 6814 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3GKE Resolution: 2.1→36 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 11.29 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.209 / ESU R Free: 0.19 / 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: 40.721 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→36 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1988 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.1→2.16 Å / Total num. of bins used: 20
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