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Yorodumi- PDB-8jua: Multifunctional cytochrome P450 enzyme IkaD from Streptomyces sp.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jua | |||||||||
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Title | Multifunctional cytochrome P450 enzyme IkaD from Streptomyces sp. ZJ306, in complex with epoxyikarugamycin | |||||||||
Components | Cytochrome P450 | |||||||||
Keywords | OXIDOREDUCTASE / C-H functionalization / regioselectivity / chemoselectivity / polycyclic tetramate macrolactam (PoTeM) / cytochrome P450 enzyme | |||||||||
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 | Streptomyces sp. ZJ306 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.00001111553 Å | |||||||||
Authors | Zhang, Y.L. / Zhang, L.P. / Zhang, C.S. | |||||||||
Funding support | China, 2items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 Title: A Mechanistic Understanding of the Distinct Regio- and Chemoselectivity of Multifunctional P450s by Structural Comparison of IkaD and CftA Complexed with Common Substrates. Authors: Jiang, P. / Jin, H. / Zhang, G. / Zhang, W. / Liu, W. / Zhu, Y. / Zhang, C. / Zhang, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jua.cif.gz | 576.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jua.ent.gz | 389.3 KB | Display | PDB format |
PDBx/mmJSON format | 8jua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jua_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8jua_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8jua_validation.xml.gz | 39.4 KB | Display | |
Data in CIF | 8jua_validation.cif.gz | 59 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/8jua ftp://data.pdbj.org/pub/pdb/validation_reports/ju/8jua | HTTPS FTP |
-Related structure data
Related structure data | 8jncC 8jnoC 8jnpC 8jnqC 8jooC C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 48058.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. ZJ306 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B4ZV78 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.65 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 3.5-4M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 2→23.310357633 Å / Num. obs: 72440 / % possible obs: 99.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 19.6584059616 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.049 / Rrim(I) all: 0.115 / Χ2: 0.98 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2→2.04 Å / % possible obs: 99.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.638 / Num. measured all: 13298 / Num. unique obs: 4397 / CC1/2: 0.544 / Rpim(I) all: 0.432 / Rrim(I) all: 0.775 / Χ2: 0.95 / Net I/σ(I) obs: 1.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.00001111553→23.310357633 Å / SU ML: 0.266269390977 / Cross valid method: FREE R-VALUE / σ(F): 1.33702057403 / Phase error: 26.2912515827
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.6442843374 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.00001111553→23.310357633 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: -2.81231770447 Å / Origin y: 0.375290560333 Å / Origin z: 25.3174487241 Å
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Refinement TLS group | Selection details: all |