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Yorodumi- PDB-7tzw: The crystal structure of WT CYP199A4 bound to 4-chlorobenzoic acid -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tzw | ||||||
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Title | The crystal structure of WT CYP199A4 bound to 4-chlorobenzoic acid | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / 4-chlorobenzoic acid | ||||||
Function / homology | Function and homology information cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.462 Å | ||||||
Authors | Podgorski, M.N. / Bell, S.G. | ||||||
Funding support | Australia, 1items
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Citation | Journal: J.Inorg.Biochem. / Year: 2023 Title: Cytochrome P450-catalyzed oxidation of halogen-containing substrates. Authors: Coleman, T. / Podgorski, M.N. / Doyle, M.L. / Scaffidi-Muta, J.M. / Campbell, E.C. / 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 | 7tzw.cif.gz | 108.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tzw.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 7tzw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tzw_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7tzw_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7tzw_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 7tzw_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/7tzw ftp://data.pdbj.org/pub/pdb/validation_reports/tz/7tzw | HTTPS FTP |
-Related structure data
Related structure data | 7tzmC 7tznC 7tzxC 7tzyC 7u00C 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: 44587.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: HaA2 / Gene: RPB_3613 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2IU02 |
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-Non-polymers , 5 types, 525 molecules
#2: Chemical | ChemComp-174 / | ||
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#3: Chemical | ChemComp-HEM / | ||
#4: Chemical | ChemComp-CL / | ||
#5: Chemical | #6: 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: 34.12 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: For crystallisation, CYP199A4 was concentrated to approx. 40 mg mL-1 in 50 mM Tris buffer, pH 7.4. Crystals were obtained using the hanging-drop vapour diffusion method at 16 degrees C using ...Details: For crystallisation, CYP199A4 was concentrated to approx. 40 mg mL-1 in 50 mM Tris buffer, pH 7.4. Crystals were obtained using the hanging-drop vapour diffusion method at 16 degrees C using 1.2 microlitres of protein with 1.2 microlitres of reservoir solution and equilibrated with 500 microlitres of the same reservoir solution. The crystallisation 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: 5.00-5.75 |
-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: Feb 17, 2021 | ||||||||||||||||||||||||||||||
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: 1.46→42.95 Å / Num. obs: 56716 / % possible obs: 99.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 10.18 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.071 / Rrim(I) all: 0.186 / Net I/σ(I): 6.3 / Num. measured all: 385880 / Scaling rejects: 243 | ||||||||||||||||||||||||||||||
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: 5UVB Resolution: 1.462→35.967 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.99 / 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: 68.37 Å2 / Biso mean: 14.4613 Å2 / Biso min: 4.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.462→35.967 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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