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Yorodumi- PDB-2xdo: Structure of the Tetracycline degrading Monooxygenase TetX2 from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xdo | ||||||
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Title | Structure of the Tetracycline degrading Monooxygenase TetX2 from Bacteroides thetaiotaomicron | ||||||
Components | TETX2 PROTEIN | ||||||
Keywords | OXIDOREDUCTASE / TETRACYCLINE DEGRADATION / TIGECYCLINE / FLAVIN / BACTEROIDES FRAGILI | ||||||
Function / homology | Function and homology information tetracycline 11a-monooxygenase / monooxygenase activity / FAD binding / response to antibiotic / cytoplasm Similarity search - Function | ||||||
Biological species | BACTEROIDES THETAIOTAOMICRON (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Volkers, G. / Palm, G.J. / Wright, G.D. / Hinrichs, W. | ||||||
Citation | Journal: FEBS Lett. / Year: 2011 Title: Structural Basis for a New Tetracycline Resistance Mechanism Relying on the Tetx Monooxygenase. Authors: Volkers, G. / Palm, G.J. / Weiss, M.S. / Wright, G.D. / Hinrichs, W. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Crystallization and Preliminary X-Ray Crystallographic Analysis of the Tetracycline- Degrading Monooxygenase Tetx2 from Bacteroides Thetaiotaomicron. Authors: Volkers, G. / Schuldt, L. / Palm, G.J. / Wright, G.D. / Hinrichs, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xdo.cif.gz | 603.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xdo.ent.gz | 500.8 KB | Display | PDB format |
PDBx/mmJSON format | 2xdo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xdo_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2xdo_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2xdo_validation.xml.gz | 63.8 KB | Display | |
Data in CIF | 2xdo_validation.cif.gz | 86.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/2xdo ftp://data.pdbj.org/pub/pdb/validation_reports/xd/2xdo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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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: 44703.395 Da / Num. of mol.: 4 / Fragment: FAD-BINDING DOMAIN, RESIDUES 11-388 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93L51 #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-SO4 / #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: 2.46 Å3/Da / Density % sol: 49.97 % / Description: NONE |
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Crystal grow | Details: 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE PH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.918 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 13, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→49.06 Å / Num. obs: 91733 / % possible obs: 92.2 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.09→2.2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 64 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SELENOMETHIONINE DERIVATIVE Resolution: 2.09→40.54 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.029 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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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: 39.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→40.54 Å
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Refine LS restraints |
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