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Yorodumi- PDB-8hgt: Crystal structure of the CYP153A mutant V456A from Marinobacter a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hgt | ||||||
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Title | Crystal structure of the CYP153A mutant V456A from Marinobacter aquaeolei | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / CYP153A | ||||||
Function / homology | Function and homology information 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 | Marinobacter nauticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Jiang, Y. / Tian, X. / Cong, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: Enabling Peroxygenase Activity in Cytochrome P450 Monooxygenases by Engineering Hydrogen Peroxide Tunnels. Authors: Zhao, P. / Kong, F. / Jiang, Y. / Qin, X. / Tian, X. / Cong, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hgt.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hgt.ent.gz | 77.9 KB | Display | PDB format |
PDBx/mmJSON format | 8hgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/8hgt ftp://data.pdbj.org/pub/pdb/validation_reports/hg/8hgt | HTTPS FTP |
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-Related structure data
Related structure data | 8hgcC 5fygS S: Starting model for refinement 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: 55250.988 Da / Num. of mol.: 1 / Mutation: V456A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marinobacter nauticus (bacteria) / Gene: DET51_1164 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A368UNN3 |
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#2: Chemical | ChemComp-HEM / |
#3: 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 Å3/Da / Density % sol: 38.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2M Li2SO4, 0.1M HEPES 7.0, 26% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 14, 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: 1.78→50 Å / Num. obs: 25202 / % possible obs: 96.6 % / Redundancy: 3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.064 / Rrim(I) all: 0.112 / Χ2: 0.802 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.428 / Num. unique obs: 2064 / CC1/2: 0.868 / Rpim(I) all: 0.283 / Rrim(I) all: 0.515 / Χ2: 0.447 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FYG Resolution: 2.06→31.38 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 23.97 / 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: 2.06→31.38 Å
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Refine LS restraints |
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LS refinement shell |
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