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Yorodumi- PDB-7r8s: The crystal structure of CYP199A4 bound to 4-n-propylbenzoic acid -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r8s | ||||||
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Title | The crystal structure of CYP199A4 bound to 4-n-propylbenzoic acid | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / 4-n-propylbenzoic acid / hydroxylation / desaturation | ||||||
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 | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.366 Å | ||||||
Authors | Podgorski, M.N. / Bell, S.G. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Chem Asian J / Year: 2022 Title: Exploring the Factors which Result in Cytochrome P450 Catalyzed Desaturation Versus Hydroxylation. Authors: Coleman, T. / Doherty, D.Z. / Zhang, T. / Podgorski, M.N. / Qiao, R. / Lee, J.H.Z. / Bruning, J.B. / De Voss, J.J. / Zhou, W. / 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 | 7r8s.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r8s.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 7r8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/7r8s ftp://data.pdbj.org/pub/pdb/validation_reports/r8/7r8s | HTTPS FTP |
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-Related structure data
Related structure data | 7udfC 8e5jC 5uvbS 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: 44587.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (strain HaA2) (phototrophic) Strain: HaA2 / Gene: RPB_3613 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2IU02 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-8ZU / |
#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: 2.02 Å3/Da / Density % sol: 39.14 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.2 M magnesium acetate, 100 mM Bis-Tris (adjusted with acetic acid to pH 5.0-5.75), 20-32% w/v PEG3350 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: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2020 | ||||||||||||||||||||||||||||||
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: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.366→44.09 Å / Num. obs: 74479 / % possible obs: 98.6 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.036 / Rrim(I) all: 0.092 / Net I/σ(I): 13 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5UVB Resolution: 1.366→44.088 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.06 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.24 Å2 / Biso mean: 15.3475 Å2 / Biso min: 6.18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.366→44.088 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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