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Yorodumi- PDB-8gdi: X-ray crystal structure of CYP124A1 from Mycobacterium Marinum in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gdi | ||||||
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Title | X-ray crystal structure of CYP124A1 from Mycobacterium Marinum in complex with 7-ketocholesterol | ||||||
Components | Cytochrome P450 124A1 | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / ligand bound | ||||||
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 | Mycobacterium marinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Ghith, A. / Bruning, J.B. / Bell, S.G. | ||||||
Funding support | Australia, 1items
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Citation | Journal: J.Steroid Biochem.Mol.Biol. / Year: 2023 Title: The oxidation of cholesterol derivatives by the CYP124 and CYP142 enzymes from Mycobacterium marinum. Authors: Ghith, A. / Bruning, J.B. / 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 | 8gdi.cif.gz | 114.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gdi.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 8gdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/8gdi ftp://data.pdbj.org/pub/pdb/validation_reports/gd/8gdi | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47313.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / Gene: cyp124A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2HHT9 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-0GV / ( |
#4: 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: 2.49 Å3/Da / Density % sol: 50.66 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 0.20 M ammonium sulfate, 20% w/v polyethylene glycol 3350, pH 6.1 |
-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: Feb 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→37.5 Å / Num. obs: 44725 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.033 / Rrim(I) all: 0.123 / Χ2: 0.93 / Net I/σ(I): 13.8 / Num. measured all: 602711 |
Reflection shell | Resolution: 1.81→1.85 Å / % possible obs: 99.8 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.756 / Num. measured all: 36000 / Num. unique obs: 2599 / CC1/2: 0.907 / Rpim(I) all: 0.21 / Rrim(I) all: 0.785 / Χ2: 0.63 / Net I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→37.5 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.63 / 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: 1.81→37.5 Å
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Refine LS restraints |
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LS refinement shell |
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