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Yorodumi- PDB-7tlo: X-ray crystal structure of substrate free cytochrome P450 CYP142A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tlo | ||||||
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Title | X-ray crystal structure of substrate free cytochrome P450 CYP142A3 from Mycobacterium Marinum | ||||||
Components | Cytochrome P450 142A3 | ||||||
Keywords | OXIDOREDUCTASE / substrate free | ||||||
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 marinum ATCC BAA-535 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Ghith, A. / Bruning, J.B. / Bell, S.G. | ||||||
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 | 7tlo.cif.gz | 192.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tlo.ent.gz | 147.7 KB | Display | PDB format |
PDBx/mmJSON format | 7tlo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tlo_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7tlo_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7tlo_validation.xml.gz | 38.9 KB | Display | |
Data in CIF | 7tlo_validation.cif.gz | 59.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/7tlo ftp://data.pdbj.org/pub/pdb/validation_reports/tl/7tlo | HTTPS FTP |
-Related structure data
Related structure data | 7sh5C 7smzC 2xkrS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45451.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium marinum ATCC BAA-535 (bacteria) Strain: ATCC BAA-535 / Gene: cyp142, MMRN_53720 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Z5YMP0 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | 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: 43 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 6.5 Details: 0.1M Sodium Cacodylate Trihdyrate pH 6.5, 0.2M Sodium Acetate Trihdrate, 30% w/v Polyethylene glycol 8000 |
-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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→46.17 Å / Num. obs: 110811 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.031 / Rrim(I) all: 0.082 / Net I/σ(I): 11.9 / Num. measured all: 777196 / Scaling rejects: 70 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XKR Resolution: 1.55→36.31 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.84 / 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: 71.13 Å2 / Biso mean: 26.5953 Å2 / Biso min: 11.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→36.31 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
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