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Yorodumi- PDB-8hos: Crystal structure of the P450 BM3 heme domain mutant F87A in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hos | |||||||||
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Title | Crystal structure of the P450 BM3 heme domain mutant F87A in complex with Im-C6-Phe(4NO2)-Tyr | |||||||||
Components |
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Keywords | OXIDOREDUCTASE / Dual-functional small molecule / P450 heme domain | |||||||||
Function / homology | Function and homology information NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / unspecific monooxygenase / aromatase activity / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / cytosol Similarity search - Function | |||||||||
Biological species | Priestia megaterium (bacteria) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | |||||||||
Authors | Jiang, Y. / Dong, S. / Feng, Y. / Cong, Z. | |||||||||
Funding support | China, 2items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 Title: Anchoring a Structurally Editable Proximal Cofactor-like Module to Construct an Artificial Dual-center Peroxygenase. Authors: Qin, X. / Jiang, Y. / Yao, F. / Chen, J. / Kong, F. / Zhao, P. / Jin, L. / Cong, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hos.cif.gz | 210.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hos.ent.gz | 164.6 KB | Display | PDB format |
PDBx/mmJSON format | 8hos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hos_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8hos_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8hos_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 8hos_validation.cif.gz | 60.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/8hos ftp://data.pdbj.org/pub/pdb/validation_reports/ho/8hos | HTTPS FTP |
-Related structure data
Related structure data | 7y0tC 8honC 8hopC 8hoqC 8horC 8houC 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: 53352.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Priestia megaterium (bacteria) / Gene: BTA37_15100 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A1Q8UP87, unspecific monooxygenase, NADPH-hemoprotein reductase #2: Protein/peptide | Mass: 537.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: 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: 2.53 Å3/Da / Density % sol: 51.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.38M MgCl2, 0.1M Tris 8.5, 12-18% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→73.67 Å / Num. obs: 94570 / % possible obs: 98.8 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.038 / Rrim(I) all: 0.07 / Χ2: 0.88 / Net I/σ(I): 10.3 / Num. measured all: 308700 |
Reflection shell | Resolution: 1.82→1.92 Å / % possible obs: 99.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.389 / Num. measured all: 40667 / Num. unique obs: 13817 / CC1/2: 0.864 / Rpim(I) all: 0.263 / Rrim(I) all: 0.471 / Χ2: 0.64 / Net I/σ(I) obs: 2.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→46.72 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.28 / 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: 1.82→46.72 Å
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Refine LS restraints |
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LS refinement shell |
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