+Open data
-Basic information
Entry | Database: PDB / ID: 8f91 | |||||||||
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Title | OxyB, a cytochrome P450 involved in keratinimicin biosynthesis | |||||||||
Components | OxyB | |||||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / monooxygenase / keratinimicin | |||||||||
Function / homology | Function and homology information 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 keratiniphila (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Ireland, K.A. / Davis, K.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acs Chem.Biol. / Year: 2023 Title: Robust Chemoenzymatic Synthesis of Keratinimicin Aglycone Analogues Facilitated by the Structure and Selectivity of OxyB. Authors: Hauser, N. / Ireland, K.A. / Chioti, V.T. / Forneris, C.C. / Davis, K.M. / Seyedsayamdost, M.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f91.cif.gz | 92.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f91.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 8f91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f91_validation.pdf.gz | 785.9 KB | Display | wwPDB validaton report |
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Full document | 8f91_full_validation.pdf.gz | 791.3 KB | Display | |
Data in XML | 8f91_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 8f91_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/8f91 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/8f91 | HTTPS FTP |
-Related structure data
Related structure data | 5ex6S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46425.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amycolatopsis keratiniphila (bacteria) / Strain: NRRL B24117 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A385L3H2 |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8 ammonium citrate tribasic, pH 7 / Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 6, 2022 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→56.62 Å / Num. obs: 12403 / % possible obs: 99.95 % / Redundancy: 2 % / Biso Wilson estimate: 67.47 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0177 / Rpim(I) all: 0.0177 / Rrim(I) all: 0.02503 / Net I/σ(I): 20.95 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2136 / Mean I/σ(I) obs: 3.21 / Num. unique obs: 1208 / CC1/2: 0.829 / CC star: 0.952 / Rpim(I) all: 0.2136 / Rrim(I) all: 0.302 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5EX6 Resolution: 2.8→56.62 Å / SU ML: 0.3824 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1207 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.45 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→56.62 Å
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Refine LS restraints |
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LS refinement shell |
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