+
Open data
-
Basic information
Entry | Database: PDB / ID: 6yct | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of GcoA F169A_T296S bound to p-vanillin | |||||||||
![]() | Cytochrome P450 | |||||||||
![]() | 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 | ![]() ![]() ![]() | |||||||||
![]() | Hinchen, D.J. / Mallinson, S.J.B. / Allen, M.D. / Ellis, E.S. / Beckham, G.T. / DuBois, J.L. / McGeehan, J.E. | |||||||||
Funding support | ![]() ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 120.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 72.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 383.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 387.9 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ychC ![]() 6yciC ![]() 6ycjC ![]() 6yckC ![]() 6yclC ![]() 6ycmC ![]() 6ycnC ![]() 6ycoC ![]() 6ycpC ![]() 5ncbS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 45362.656 Da / Num. of mol.: 1 / Mutation: F169A_T296S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 39116 / 75iv2 / Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-EPE / |
#3: Chemical | ChemComp-V55 / |
#4: Chemical | ChemComp-HEC / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.19 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→47.41 Å / Num. obs: 25466 / % possible obs: 99.76 % / Redundancy: 2 % / Biso Wilson estimate: 36.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02076 / Net I/σ(I): 25.64 |
Reflection shell | Resolution: 2.39→2.48 Å / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 6.03 / Num. unique obs: 2445 / CC1/2: 0.954 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5NCB Resolution: 2.39→47.41 Å / SU ML: 0.2217 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.5734
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.39→47.41 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|