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Yorodumi- PDB-8vf0: The crystal structure of QE CYP199A4 bound to 4-methoxybenzoic acid -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vf0 | ||||||
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Title | The crystal structure of QE CYP199A4 bound to 4-methoxybenzoic acid | ||||||
Components | Cytochrome P450 enzyme (CYP199A4) | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 peroxygenase | ||||||
Function / homology | 4-METHOXYBENZOIC ACID / PROTOPORPHYRIN IX CONTAINING FE Function and homology information | ||||||
Biological species | Rhodopseudomonas palustris HaA2 (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.028 Å | ||||||
Authors | Podgorski, M.N. / Bell, S.G. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Acs Catalysis / Year: 2024 Title: Engineering Peroxygenase Activity into Cytochrome P450 Monooxygenases through Modification of the Oxygen Binding Region Authors: Podgorski, M.N. / Akter, J. / Churchman, L.R. / Bruning, J.B. / De Voss, J.J. / Bell, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vf0.cif.gz | 100.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vf0.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 8vf0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vf0_validation.pdf.gz | 1022.9 KB | Display | wwPDB validaton report |
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Full document | 8vf0_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8vf0_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 8vf0_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/8vf0 ftp://data.pdbj.org/pub/pdb/validation_reports/vf/8vf0 | HTTPS FTP |
-Related structure data
Related structure data | 8vf3C 8vfpC 8vfrC 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: 44628.480 Da / Num. of mol.: 1 / Mutation: D251Q, T252E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris HaA2 (phototrophic) Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: Chemical | ChemComp-ANN / |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-CL / |
#5: 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: 2.03 Å3/Da / Density % sol: 39.26 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: The crystallization buffer was 100 mM Bis-Tris buffer (adjusted to pH 5.0-5.75 with acetic acid), 0.2 M magnesium acetate and 20-32% PEG 3350 PH range: 5.0-5.75 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95373 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 14, 2022 |
Radiation | Monochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.028→44.63 Å / Num. obs: 23301 / % possible obs: 99.4 % / Redundancy: 6.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.278 / Rpim(I) all: 0.114 / Rrim(I) all: 0.301 / Χ2: 0.56 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.03→2.08 Å / % possible obs: 95.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 1.79 / Num. measured all: 10671 / Num. unique obs: 1649 / CC1/2: 0.579 / Rpim(I) all: 0.748 / Rrim(I) all: 1.944 / Χ2: 0.58 / Net I/σ(I) obs: 0.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.028→44.626 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.89 / 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: 2.028→44.626 Å
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Refine LS restraints |
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LS refinement shell |
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