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Open data
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Basic information
Entry | Database: PDB / ID: 6ycm | |||||||||
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Title | Crystal structure of GcoA T296S bound to p-vanillin | |||||||||
![]() | Aromatic O-demethylase, cytochrome P450 subunit | |||||||||
![]() | OXIDOREDUCTASE / Aromatic catabolism / cytochrome P450 / lignin valorization / protein engineering | |||||||||
Function / homology | ![]() Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / : / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mallinson, S.J.B. / Hinchen, D.J. / Ellis, E.S. / Beckham, G.T. / DuBois, J.L. / McGeehan, J.E. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Engineering a Cytochrome P450 for Demethylation of Lignin-Derived Aromatic Aldehydes. Authors: Ellis, E.S. / Hinchen, D.J. / Bleem, A. / Bu, L. / Mallinson, S.J.B. / Allen, M.D. / Streit, B.R. / Machovina, M.M. / Doolin, Q.V. / Michener, W.E. / Johnson, C.W. / Knott, B.C. / Beckham, G. ...Authors: Ellis, E.S. / Hinchen, D.J. / Bleem, A. / Bu, L. / Mallinson, S.J.B. / Allen, M.D. / Streit, B.R. / Machovina, M.M. / Doolin, Q.V. / Michener, W.E. / Johnson, C.W. / Knott, B.C. / Beckham, G.T. / McGeehan, J.E. / DuBois, J.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.9 KB | Display | ![]() |
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PDB format | ![]() | 80.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 377.2 KB | Display | ![]() |
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Full document | ![]() | 379.1 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ychC ![]() 6yciC ![]() 6ycjC ![]() 6yckC ![]() 6yclC ![]() 6ycnC ![]() 6ycoC ![]() 6ycpC ![]() 6yctC ![]() 5ncbS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 45438.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 39116 / 75iv2 / Gene: gcoA / Production host: ![]() ![]() References: UniProt: P0DPQ7, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one ...References: UniProt: P0DPQ7, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-V55 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Na Malonate, HEPES, p-vanillin |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→52.02 Å / Num. obs: 83956 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 22.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.52 |
Reflection shell | Resolution: 1.6→1.657 Å / Rmerge(I) obs: 1.118 / Num. unique obs: 8286 / CC1/2: 0.898 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5NCB Resolution: 1.6→52.02 Å / SU ML: 0.2075 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.8354 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→52.02 Å
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Refine LS restraints |
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LS refinement shell |
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