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Yorodumi- PDB-6net: FAD-dependent monooxygenase TropB from T. stipitatus substrate complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 6net | |||||||||
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Title | FAD-dependent monooxygenase TropB from T. stipitatus substrate complex | |||||||||
Components | FAD-dependent monooxygenase tropB | |||||||||
Keywords | FLAVOPROTEIN / oxidative dearomatization | |||||||||
Function / homology | Function and homology information Oxidoreductases / secondary metabolite biosynthetic process / monooxygenase activity / FAD binding / membrane Similarity search - Function | |||||||||
Biological species | Talaromyces stipitatus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Rodriguez Benitez, A. / Tweedy, S.E. / Baker Dockrey, S.A. / Lukowski, A.L. / Wymore, T. / Khare, D. / Brooks, C.L. / Palfey, B.A. / Smith, J.L. / Narayan, A.R.H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acs Catalysis / Year: 2019 Title: Structural basis for selectivity in flavin-dependent monooxygenase-catalyzed oxidative dearomatization. Authors: Rodriguez Benitez, A. / Tweedy, S.E. / Baker Dockrey, S.A. / Lukowski, A.L. / Wymore, T. / Khare, D. / Brooks 3rd, C.L. / Palfey, B.A. / Smith, J.L. / Narayan, A.R.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6net.cif.gz | 410.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6net.ent.gz | 275.2 KB | Display | PDB format |
PDBx/mmJSON format | 6net.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/6net ftp://data.pdbj.org/pub/pdb/validation_reports/ne/6net | HTTPS FTP |
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-Related structure data
Related structure data | 6nesSC 6neuC 6nevC 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 49941.824 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Talaromyces stipitatus (strain ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006) (fungus) Strain: ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006 / Gene: tropB, tsL1, TSTA_117740 / Production host: Escherichia coli (E. coli) / References: UniProt: B8M9J8 |
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-Non-polymers , 5 types, 133 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #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: 2.78 Å3/Da / Density % sol: 55.81 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 1.11 M ammonium tartrate dibasic, 6% hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.245→45.96 Å / Num. obs: 47286 / % possible obs: 99.8 % / Redundancy: 13.3 % / Biso Wilson estimate: 51.95 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.19 / Net I/σ(I): 1 |
Reflection shell | Resolution: 2.245→2.325 Å / Rmerge(I) obs: 2.457 / CC1/2: 0.41 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NES Resolution: 2.25→45.96 Å / SU ML: 0.3754 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.2893
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→45.96 Å
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Refine LS restraints |
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LS refinement shell |
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