+Open data
-Basic information
Entry | Database: PDB / ID: 1pkf | ||||||
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Title | Crystal Structure of Epothilone D-bound Cytochrome P450epoK | ||||||
Components | cytochrome p450EpoK | ||||||
Keywords | OXIDOREDUCTASE / CYTOCHROME P450EPOK / HEME-ENZYME | ||||||
Function / homology | Function and homology information epothilone biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen into the other donor / 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 | Sorangium cellulosum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Nagano, S. / Li, H. / Shimizu, H. / Nishida, C. / Ogura, H. / Ortiz de Montellano, P.R. / Poulos, T.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal Structures of Epothilone D-bound, Epothilone B-bound, and Substrate-free Forms of Cytochrome P450epoK Authors: Nagano, S. / Li, H. / Shimizu, H. / Nishida, C. / Ogura, H. / Ortiz de Montellano, P.R. / Poulos, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pkf.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pkf.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/1pkf ftp://data.pdbj.org/pub/pdb/validation_reports/pk/1pkf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46823.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sorangium cellulosum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KIZ4 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-EPD / |
#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: 2.46 Å3/Da / Density % sol: 50.06 % | ||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.4 Details: PEG 550, Glycine, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 23K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / Method: vapor diffusion | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2002 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 25935 / % possible obs: 96.2 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 33.9 |
Reflection shell | Resolution: 2.1→2.154 Å / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1348 / % possible all: 96.2 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 50 Å / Num. obs: 27331 / Num. measured all: 167058 |
Reflection shell | *PLUS % possible obs: 95.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.421 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.099 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 50 Å / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.216 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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