+Open data
-Basic information
Entry | Database: PDB / ID: 6hqn | ||||||||||||
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Title | Crystal structure of GcoA F169L bound to guaiacol | ||||||||||||
Components | Cytochrome P450 | ||||||||||||
Keywords | OXIDOREDUCTASE / cytochrome / P450 / lignin. | ||||||||||||
Function / homology | Function and homology information 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 / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||||||||
Biological species | Amycolatopsis sp. ATCC 39116 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||||||||
Authors | Mallinson, S.J.B. / Hinchen, D.J. / Allen, M.D. / Johnson, C.W. / Beckham, G.T. / McGeehan, J.E. | ||||||||||||
Funding support | United Kingdom, United States, 3items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hqn.cif.gz | 193.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hqn.ent.gz | 152.9 KB | Display | PDB format |
PDBx/mmJSON format | 6hqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/6hqn ftp://data.pdbj.org/pub/pdb/validation_reports/hq/6hqn | HTTPS FTP |
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-Related structure data
Related structure data | 6hqkC 6hqlC 6hqmC 6hqoC 6hqpC 6hqqC 6hqrC 6hqsC 6hqtC 5ncbS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 45264.594 Da / Num. of mol.: 1 / Mutation: F169L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amycolatopsis sp. ATCC 39116 (bacteria) Gene: AMETH_3834 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A076MY51, UniProt: P0DPQ7*PLUS |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-JZ3 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.09 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: Sodium malonate, HEPES, guaiacol. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
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: 1.87→76.08 Å / Num. obs: 52238 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.999 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.87→1.92 Å / Mean I/σ(I) obs: 2.4 / CC1/2: 0.808 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NCB Resolution: 1.87→73.539 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→73.539 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: 46.551 Å / Origin y: 80.5115 Å / Origin z: 40.9768 Å
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Refinement TLS group | Selection details: all |