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Yorodumi- PDB-5oms: Crystal structure of Amycolatopsis cytochrome P450 GcoA in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oms | ||||||||||||
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Title | Crystal structure of Amycolatopsis cytochrome P450 GcoA in complex with guaethol. | ||||||||||||
Components | Cytochrome P450 | ||||||||||||
Keywords | OXIDOREDUCTASE / Cytochrome / P450 / guaiacol / lignin / CYP255A / Amycolatopsis / heme / haem / guaethol | ||||||||||||
Function / homology | Function and homology information cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||||||||
Biological species | Amycolatopsis sp. ATCC 39116 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||||||||
Authors | Mallinson, S.J.B. / Johnson, C.W. / Neidle, E.L. / Beckham, G.T. / McGeehan, J.E. | ||||||||||||
Funding support | United Kingdom, United States, 3items
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Citation | Journal: Nat Commun / Year: 2018 Title: A promiscuous cytochrome P450 aromatic O-demethylase for lignin bioconversion. Authors: Mallinson, S.J.B. / Machovina, M.M. / Silveira, R.L. / Garcia-Borras, M. / Gallup, N. / Johnson, C.W. / Allen, M.D. / Skaf, M.S. / Crowley, M.F. / Neidle, E.L. / Houk, K.N. / Beckham, G.T. / ...Authors: Mallinson, S.J.B. / Machovina, M.M. / Silveira, R.L. / Garcia-Borras, M. / Gallup, N. / Johnson, C.W. / Allen, M.D. / Skaf, M.S. / Crowley, M.F. / Neidle, E.L. / Houk, K.N. / Beckham, G.T. / DuBois, J.L. / McGeehan, J.E. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oms.cif.gz | 180.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oms.ent.gz | 142.3 KB | Display | PDB format |
PDBx/mmJSON format | 5oms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oms_validation.pdf.gz | 863.9 KB | Display | wwPDB validaton report |
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Full document | 5oms_full_validation.pdf.gz | 867.4 KB | Display | |
Data in XML | 5oms_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 5oms_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/5oms ftp://data.pdbj.org/pub/pdb/validation_reports/om/5oms | HTTPS FTP |
-Related structure data
Related structure data | 5ncbSC 5ogxC 5omrC 5omuC 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: 45452.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amycolatopsis sp. ATCC 39116 (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: A0A3B6UEE9*PLUS |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-261 / |
#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: 3.43 Å3/Da / Density % sol: 64.12 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 2.4M sodium malonate; 0.2M guaethol (in DMSO) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→47.46 Å / Num. obs: 46675 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.018 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.773 / Num. unique obs: 3389 / CC1/2: 0.863 / Rpim(I) all: 0.327 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NCB Resolution: 1.95→47.46 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→47.46 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: 47.4011 Å / Origin y: 80.7965 Å / Origin z: 41.9719 Å
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Refinement TLS group | Selection details: all |