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Yorodumi- PDB-8hny: Crystal structure of cytochrome P450 NasF5053 mutant E73S complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hny | ||||||
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Title | Crystal structure of cytochrome P450 NasF5053 mutant E73S complexed with 5FCWP | ||||||
Components | Cytochrome P450-F5053 | ||||||
Keywords | OXIDOREDUCTASE / P450 | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / 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. NRRL F-5053 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Ma, B.D. / Tian, W. / Qu, X. / Kong, X.D. | ||||||
Funding support | China, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 Title: Engineering the Substrate Specificity of a P450 Dimerase Enables the Collective Biosynthesis of Heterodimeric Tryptophan-Containing Diketopiperazines. Authors: Sun, C. / Ma, B.D. / Li, G. / Tian, W. / Yang, L. / Peng, H. / Lin, Z. / Deng, Z. / Kong, X.D. / Qu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hny.cif.gz | 96.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hny.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 8hny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hny_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8hny_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8hny_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 8hny_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/8hny ftp://data.pdbj.org/pub/pdb/validation_reports/hn/8hny | HTTPS FTP |
-Related structure data
Related structure data | 8hnzC 8ho0C 8ho1C 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
#1: Protein | Mass: 43417.039 Da / Num. of mol.: 1 / Mutation: E73S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. NRRL F-5053 (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: A0A8I3B027 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-2IV / ( |
#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: 2.09 Å3/Da / Density % sol: 41.22 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 18-22% PEG3350 (w/v), 0.2 M CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97854 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 29, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97854 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→95.09 Å / Num. obs: 21007 / % possible obs: 95.6 % / Redundancy: 12.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.083 / Rrim(I) all: 0.216 / Χ2: 1 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.301 / Num. unique obs: 1737 / CC1/2: 0.809 / Rpim(I) all: 0.545 / Χ2: 0.95 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→38.51 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.18 / 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: 2.1→38.51 Å
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Refine LS restraints |
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LS refinement shell |
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