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Yorodumi- PDB-7tp5: The crystal structure of T252E CYP199A4 bound to 4-ethylthiobenzo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tp5 | ||||||
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Title | The crystal structure of T252E CYP199A4 bound to 4-ethylthiobenzoic acid | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / peroxygenase / sulfoxidation | ||||||
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 HaA2 (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.655 Å | ||||||
Authors | Podgorski, M. / Bell, S.G. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Chemistry / Year: 2022 Title: Investigating the Active Oxidants Involved in Cytochrome P450 Catalyzed Sulfoxidation Reactions. Authors: Podgorski, M.N. / Coleman, T. / 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 | 7tp5.cif.gz | 105 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tp5.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 7tp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/7tp5 ftp://data.pdbj.org/pub/pdb/validation_reports/tp/7tp5 | HTTPS FTP |
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-Related structure data
Related structure data | 7tp6C 7tqmC 8dybC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44615.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris HaA2 (phototrophic) Strain: HaA2 / Gene: RPB_3613 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2IU02 |
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-Non-polymers , 6 types, 401 molecules
#2: Chemical | ChemComp-HEM / | ||
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#3: Chemical | ChemComp-81M / | ||
#4: Chemical | ChemComp-CL / | ||
#5: Chemical | ChemComp-MG / | ||
#6: Chemical | #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: 1.87 Å3/Da / Density % sol: 34.23 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 100 mM Bis-Tris (adjusted to pH 5.0-5.75 with acetic acid), 0.2 M magnesium acetate, 20-32% 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: MX1 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 5, 2018 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.655→40.7 Å / Num. obs: 31873 / % possible obs: 81.1 % / Redundancy: 5 % / Biso Wilson estimate: 13.11 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.067 / Rrim(I) all: 0.161 / Net I/σ(I): 9.3 | ||||||||||||||||||||||||||||||
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: 1.655→40.697 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.38 / 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: 70.18 Å2 / Biso mean: 16.5554 Å2 / Biso min: 5.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.655→40.697 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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