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Yorodumi- PDB-6dcd: Mycobacterium marinum cytochrome P450 CYP150A6 in the substrate-f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dcd | ||||||
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Title | Mycobacterium marinum cytochrome P450 CYP150A6 in the substrate-free form | ||||||
Components | Cytochrome P450 150A6 Cyp150A6 | ||||||
Keywords | OXIDOREDUCTASE / cytochrome P450 / monooxygenase / heme protein | ||||||
Function / homology | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / Cytochrome P450, B-class / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / iron ion binding / heme binding / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 150A6 Cyp150A6 Function and homology information | ||||||
Biological species | Mycobacterium marinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å | ||||||
Authors | Child, S.A. / Bruning, J.B. / Bell, S.G. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Biochim Biophys Acta Gen Subj / Year: 2019 Title: The characterisation of two members of the cytochrome P450 CYP150 family: CYP150A5 and CYP150A6 from Mycobacterium marinum. Authors: Child, S.A. / Flint, K.L. / 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 | 6dcd.cif.gz | 195.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dcd.ent.gz | 154.8 KB | Display | PDB format |
PDBx/mmJSON format | 6dcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dcd_validation.pdf.gz | 811.7 KB | Display | wwPDB validaton report |
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Full document | 6dcd_full_validation.pdf.gz | 815.5 KB | Display | |
Data in XML | 6dcd_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 6dcd_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/6dcd ftp://data.pdbj.org/pub/pdb/validation_reports/dc/6dcd | HTTPS FTP |
-Related structure data
Similar structure data |
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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: 47778.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / M / Gene: cyp150A6, MMAR_4694 / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HFD6 |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.46 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.7 Details: 0.2 M ammonium phosphate, 20% w/v polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9857 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 13, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9857 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→48.47 Å / Num. obs: 74838 / % possible obs: 100 % / Redundancy: 22 % / Biso Wilson estimate: 16.72 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.262 / Rpim(I) all: 0.057 / Rrim(I) all: 0.269 / Net I/σ(I): 11.7 / Num. measured all: 1649781 / Scaling rejects: 241 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→48.47 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.98 Å2 / Biso mean: 25.4974 Å2 / Biso min: 8.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→48.47 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 7.1475 Å / Origin y: 37.2014 Å / Origin z: 49.4131 Å
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Refinement TLS group |
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