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Yorodumi- PDB-4a6n: STRUCTURE OF THE TETRACYCLINE DEGRADING MONOOXYGENASE TETX IN COM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a6n | ||||||
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Title | STRUCTURE OF THE TETRACYCLINE DEGRADING MONOOXYGENASE TETX IN COMPLEX WITH TIGECYCLINE | ||||||
Components | (TETX2 PROTEIN) x 2 | ||||||
Keywords | OXIDOREDUCTASE / ANTIBIOTIC RESISTANCE | ||||||
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: 2.3 Å | ||||||
Authors | Volkers, G. / Palm, G.J. / Weiss, M.S. / Hinrichs, W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Putative Dioxygen-Binding Sites and Recognition of Tigecycline and Minocycline in the Tetracycline-Degrading Monooxygenase Tetx Authors: Volkers, G. / Damas, J.M. / Palm, G.J. / Panjikar, S. / Soares, C.M. / Hinrichs, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a6n.cif.gz | 597.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a6n.ent.gz | 496.1 KB | Display | PDB format |
PDBx/mmJSON format | 4a6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a6n_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 4a6n_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 4a6n_validation.xml.gz | 60.1 KB | Display | |
Data in CIF | 4a6n_validation.cif.gz | 78.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/4a6n ftp://data.pdbj.org/pub/pdb/validation_reports/a6/4a6n | HTTPS FTP |
-Related structure data
Related structure data | 4a99C 4guvC 2xdoS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 44703.461 Da / Num. of mol.: 1 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 |
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#2: Protein | Mass: 44703.395 Da / Num. of mol.: 3 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 |
-Non-polymers , 4 types, 229 molecules
#3: Chemical | ChemComp-FAD / #4: Chemical | ChemComp-T1C / #5: Chemical | ChemComp-SO4 / #6: 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: 2.44 Å3/Da / Density % sol: 49.6 % / Description: NONE |
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Crystal grow | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→81.897 Å / Num. obs: 75167 / % possible obs: 96 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XDO Resolution: 2.3→81.9 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 15.307 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.377 / ESU R Free: 0.255 / 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: 61.598 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→81.9 Å
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Refine LS restraints |
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