+Open data
-Basic information
Entry | Database: PDB / ID: 8fz8 | ||||||
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Title | Structure of cytochrome P450sky2 | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / P450sky2 / epoxidation | ||||||
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 | Streptomyces nodosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||
Authors | Murarka, V.C. / Poulos, T.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Org.Biomol.Chem. / Year: 2024 Title: Biosynthesis of a new skyllamycin in Streptomyces nodosus : a cytochrome P450 forms an epoxide in the cinnamoyl chain. Authors: Song, Y. / Amaya, J.A. / Murarka, V.C. / Mendez, H. / Hogan, M. / Muldoon, J. / Evans, P. / Ortin, Y. / Kelly, S.L. / Lamb, D.C. / Poulos, T.L. / Caffrey, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fz8.cif.gz | 192.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fz8.ent.gz | 150.6 KB | Display | PDB format |
PDBx/mmJSON format | 8fz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/8fz8 ftp://data.pdbj.org/pub/pdb/validation_reports/fz/8fz8 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45184.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces nodosus (bacteria) / Gene: CP978_29155 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5P2W9N6 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-OCA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonium acetate, 0.1 M Tris:HCl buffer pH 8.5, 25% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→52.29 Å / Num. obs: 64363 / % possible obs: 96.6 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.03 / Rrim(I) all: 0.063 / Χ2: 0.99 / Net I/σ(I): 11.9 / Num. measured all: 253881 |
Reflection shell | Resolution: 1.43→1.45 Å / % possible obs: 97.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.418 / Num. measured all: 12781 / Num. unique obs: 3208 / CC1/2: 0.871 / Rpim(I) all: 0.238 / Rrim(I) all: 0.483 / Χ2: 0.64 / Net I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→35.84 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→35.84 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: 9.0878 Å / Origin y: 9.7804 Å / Origin z: 4.4395 Å
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Refinement TLS group | Selection details: all |