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Yorodumi- PDB-8vf3: The crystal structure of GALQE CYP199A4 bound to 4-methoxybenzoic acid -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vf3 | ||||||
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Title | The crystal structure of GALQE CYP199A4 bound to 4-methoxybenzoic acid | ||||||
Components | Cytochrome P450 enzyme (CYP199A4) | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 peroxygenase | ||||||
Function / homology | ACETATE ION / 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: 1.469 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 | 8vf3.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vf3.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 8vf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/8vf3 ftp://data.pdbj.org/pub/pdb/validation_reports/vf/8vf3 | HTTPS FTP |
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-Related structure data
Related structure data | 8vf0C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44628.480 Da / Num. of mol.: 1 / Mutation: A248G, G249A, 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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-Non-polymers , 6 types, 720 molecules
#2: Chemical | ChemComp-ANN / |
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#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-ACT / |
#6: Chemical | ChemComp-MG / |
#7: Water | ChemComp-HOH / |
-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: 2.04 Å3/Da / Density % sol: 39.7 % |
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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: MX2 / Wavelength: 0.95373 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2022 |
Radiation | Monochromator: Double-crystal Si(111) liquid nitrogen cooled (DC) or channel-cut Si(111) liquid nitrogen cooled (CC) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.469→45 Å / Num. obs: 60758 / % possible obs: 99.1 % / Redundancy: 5.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.049 / Rrim(I) all: 0.122 / Χ2: 0.6 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.47→1.49 Å / % possible obs: 95.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.545 / Num. measured all: 15554 / Num. unique obs: 2902 / CC1/2: 0.84 / Rpim(I) all: 0.248 / Rrim(I) all: 0.601 / Χ2: 0.6 / Net I/σ(I) obs: 2.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.469→45 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.81 / 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: 1.469→45 Å
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Refine LS restraints |
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LS refinement shell |
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