+Open data
-Basic information
Entry | Database: PDB / ID: 7epw | ||||||
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Title | Crystal structure of monooxygenase Tet(X4) with tigecycline | ||||||
Components | Flavin-dependent monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / monooxygenase / Tet(X4) / tigecycline resistance | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / monooxygenase activity / FAD binding / response to antibiotic / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å | ||||||
Authors | Cheng, Q. / Chen, S. | ||||||
Citation | Journal: Bmc Biol. / Year: 2021 Title: Structural and mechanistic basis of the high catalytic activity of monooxygenase Tet(X4) on tigecycline. Authors: Cheng, Q. / Cheung, Y. / Liu, C. / Xiao, Q. / Sun, B. / Zhou, J. / Chan, E.W.C. / Zhang, R. / Chen, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7epw.cif.gz | 95.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7epw.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 7epw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7epw_validation.pdf.gz | 935.5 KB | Display | wwPDB validaton report |
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Full document | 7epw_full_validation.pdf.gz | 933.5 KB | Display | |
Data in XML | 7epw_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 7epw_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/7epw ftp://data.pdbj.org/pub/pdb/validation_reports/ep/7epw | HTTPS FTP |
-Related structure data
Related structure data | 7epvSC 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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-Components
#1: Protein | Mass: 43343.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tet(X) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A3T0V9Y5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of ...References: UniProt: A0A3T0V9Y5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor |
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#2: Chemical | ChemComp-FDA / |
#3: Chemical | ChemComp-T1C / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 30% PEG4000, 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6 PH range: 5.4-5.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→84.35 Å / Num. obs: 23785 / % possible obs: 99.6 % / Redundancy: 36.5 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.23→2.29 Å / Rmerge(I) obs: 1.917 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1715 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EPV Resolution: 2.23→48.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.131 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.17 Å2 / Biso mean: 47.528 Å2 / Biso min: 25.84 Å2
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Refinement step | Cycle: final / Resolution: 2.23→48.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.23→2.288 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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