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Yorodumi- PDB-7sh5: Crystal structure of CYP142A3 from Mycobacterium ulcerans bound t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sh5 | ||||||
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Title | Crystal structure of CYP142A3 from Mycobacterium ulcerans bound to Cholest-4-en-3-one | ||||||
Components | Cytochrome P450 142A3 | ||||||
Keywords | LIPID BINDING PROTEIN / OXIDOREDUCTASE / P450 / heme / mono-oxygenase / lipid / catabolism / cholesterol / cholest-4-en-3-one / mycobacteria / tuberculosis / ulcerans | ||||||
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 | Mycobacterium ulcerans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Doherty, D.Z. / Bell, S.G. / Bruning, J. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2022 Title: The Structures of the Steroid Binding CYP142 Cytochrome P450 Enzymes from Mycobacterium ulcerans and Mycobacterium marinum. Authors: Ghith, A. / Doherty, D.Z. / Bruning, J.B. / Russell, R.A. / 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 | 7sh5.cif.gz | 364.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sh5.ent.gz | 294.4 KB | Display | PDB format |
PDBx/mmJSON format | 7sh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sh5_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 7sh5_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 7sh5_validation.xml.gz | 77.7 KB | Display | |
Data in CIF | 7sh5_validation.cif.gz | 112.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/7sh5 ftp://data.pdbj.org/pub/pdb/validation_reports/sh/7sh5 | HTTPS FTP |
-Related structure data
Related structure data | 7smzC 7tloC 2yooS 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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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 45362.465 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium ulcerans (bacteria) / Strain: Agy99 / Gene: cyp142A3, MUL_4077 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0PUV7 |
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-Non-polymers , 5 types, 1670 molecules
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-K2B / ( #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-ACT / #6: Water | ChemComp-HOH / | |
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-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: 2.11 Å3/Da / Density % sol: 41.77 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 0.2 M Sodium Acetate pH 5.5-6.0, 10% PEG 8000, 0.1 M Sodium cacodylate trihydrate PH range: 5.5-6.0 |
-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: 0.95 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.83→47.87 Å / Num. obs: 132141 / % possible obs: 98.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 21.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Rrim(I) all: 0.056 / Net I/σ(I): 18.2 / Num. measured all: 935212 / Scaling rejects: 7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YOO Resolution: 1.83→40.807 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.12 / 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: 83.26 Å2 / Biso mean: 25.2768 Å2 / Biso min: 8.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.83→40.807 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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