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Open data
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Basic information
Entry | Database: PDB / ID: 6hqt | ||||||||||||
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Title | Crystal structure of GcoA F169V bound to syringol | ||||||||||||
![]() | Cytochrome P450 | ||||||||||||
![]() | OXIDOREDUCTASE / cytochrome / P450 / lignin. | ||||||||||||
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. / Allen, M.D. / Johnson, C.W. / Beckham, G.T. / McGeehan, J.E. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Enabling microbial syringol conversion through structure-guided protein engineering. Authors: Machovina, M.M. / Mallinson, S.J.B. / Knott, B.C. / Meyers, A.W. / Garcia-Borras, M. / Bu, L. / Gado, J.E. / Oliver, A. / Schmidt, G.P. / Hinchen, D.J. / Crowley, M.F. / Johnson, C.W. / ...Authors: Machovina, M.M. / Mallinson, S.J.B. / Knott, B.C. / Meyers, A.W. / Garcia-Borras, M. / Bu, L. / Gado, J.E. / Oliver, A. / Schmidt, G.P. / Hinchen, D.J. / Crowley, M.F. / Johnson, C.W. / Neidle, E.L. / Payne, C.M. / Houk, K.N. / 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 | ![]() | 189.4 KB | Display | ![]() |
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PDB format | ![]() | 149.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 30 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hqkC ![]() 6hqlC ![]() 6hqmC ![]() 6hqnC ![]() 6hqoC ![]() 6hqpC ![]() 6hqqC ![]() 6hqrC ![]() 6hqsC ![]() 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: 45250.566 Da / Num. of mol.: 1 / Mutation: F169V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: AMETH_3834 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-3DM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.31 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: Sodium malonate, HEPES, syringol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 20, 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: 1.85→62 Å / Num. obs: 544478 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 1 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.85→1.9 Å / Mean I/σ(I) obs: 2.3 / CC1/2: 0.809 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5NCB Resolution: 1.85→50.504 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→50.504 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 47.2386 Å / Origin y: 80.3881 Å / Origin z: 42.2287 Å
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Refinement TLS group | Selection details: all |