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Yorodumi- PDB-8joo: Crystal structure of cytochrome P450 IkaD from Streptomyces sp. Z... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8joo | |||||||||
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Title | Crystal structure of cytochrome P450 IkaD from Streptomyces sp. ZJ306, in complex with the substrate ikarugamycin | |||||||||
Components | Cytochrome P450 | |||||||||
Keywords | OXIDOREDUCTASE / hydroxylation / polycyclic tetramate macrolactam / cytochrome P450 | |||||||||
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: 2.25 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 | 8joo.cif.gz | 479 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8joo.ent.gz | 398.2 KB | Display | PDB format |
PDBx/mmJSON format | 8joo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8joo_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8joo_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8joo_validation.xml.gz | 37.7 KB | Display | |
Data in CIF | 8joo_validation.cif.gz | 55.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/8joo ftp://data.pdbj.org/pub/pdb/validation_reports/jo/8joo | HTTPS FTP |
-Related structure data
Related structure data | 8jncC 8jnoC 8jnpC 8jnqC 8juaC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45887.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. ZJ306 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4ZV78 |
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-Non-polymers , 5 types, 654 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.96 Å3/Da / Density % sol: 58.43 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 3.5-4.0 M 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: Mar 6, 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: 2.25→19.89 Å / Num. obs: 49517 / % possible obs: 97.5 % / Redundancy: 2.8 % / CC1/2: 0.977 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.108 / Rrim(I) all: 0.193 / Χ2: 1 / Net I/σ(I): 5 / Num. measured all: 139583 |
Reflection shell | Resolution: 2.25→2.32 Å / % possible obs: 98.6 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.418 / Num. measured all: 13314 / Num. unique obs: 4579 / CC1/2: 0.79 / Rpim(I) all: 0.282 / Rrim(I) all: 0.508 / Χ2: 0.9 / Net I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→19.89 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.29 / 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: 2.25→19.89 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: -2.8714 Å / Origin y: 0.479 Å / Origin z: 25.3596 Å
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Refinement TLS group | Selection details: all |