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Yorodumi- PDB-8fjo: X-ray crystal structure of CYP124A1 from Mycobacterium Marinum in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fjo | ||||||
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Title | X-ray crystal structure of CYP124A1 from Mycobacterium Marinum in complex with farnesyl acetate | ||||||
Components | Cytochrome P450 124A1, Cyp124A1 | ||||||
Keywords | OXIDOREDUCTASE/SUBSTRATE / substrate bound / OXIDOREDUCTASE / OXIDOREDUCTASE-SUBSTRATE complex | ||||||
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: 1.69 Å | ||||||
Authors | Ghith, A. / Bruning, J.B. / Bell, S.G. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Arch.Biochem.Biophys. / Year: 2023 Title: The catalytic activity and structure of the lipid metabolizing CYP124 cytochrome P450 enzyme 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 | 8fjo.cif.gz | 109.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fjo.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 8fjo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fjo_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8fjo_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8fjo_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 8fjo_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/8fjo ftp://data.pdbj.org/pub/pdb/validation_reports/fj/8fjo | HTTPS FTP |
-Related structure data
Related structure data | 8fkbC 8floC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49289.477 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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-Non-polymers , 7 types, 259 molecules
#2: Chemical | ChemComp-HEM / | ||||||||
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#3: Chemical | ChemComp-Y7R / ( | ||||||||
#4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-NH4 / | #7: Chemical | #8: 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: 2.16 Å3/Da / Density % sol: 42.96 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 0.15 M Ammonium sulfate, 20% w/v polyethylene glycol 3,350 |
-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: Oct 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→46.78 Å / Num. obs: 46899 / % possible obs: 98.3 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.037 / Rrim(I) all: 0.096 / Χ2: 0.5 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.7→1.73 Å / % possible obs: 69.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 1.524 / Num. measured all: 8736 / Num. unique obs: 1711 / CC1/2: 0.554 / Rpim(I) all: 0.692 / Rrim(I) all: 1.681 / Χ2: 0.35 / Net I/σ(I) obs: 0.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→45.92 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 25.83 / 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: 1.69→45.92 Å
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Refine LS restraints |
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LS refinement shell |
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