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Yorodumi- PDB-3ivy: Crystal structure of Mycobacterium tuberculosis cytochrome P450 C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ivy | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis cytochrome P450 CYP125, p212121 crystal form | ||||||
Components | Cytochrome P450 CYP125 | ||||||
Keywords | OXIDOREDUCTASE / cholesterol / cytochrome P450 / tuberculosis / monooxygenase / Heme / Iron / Metal-binding | ||||||
Function / homology | Function and homology information cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] / biological process involved in interaction with host / 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 tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.352 Å | ||||||
Authors | McLean, K.J. / Levy, C. / Munro, A.W. / Leys, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: The Structure of Mycobacterium tuberculosis CYP125: molecular basis for cholesterol binding in a P450 needed for host infection. Authors: McLean, K.J. / Lafite, P. / Levy, C. / Cheesman, M.R. / Mast, N. / Pikuleva, I.A. / Leys, D. / Munro, A.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ivy.cif.gz | 213.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ivy.ent.gz | 167.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ivy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ivy_validation.pdf.gz | 803.2 KB | Display | wwPDB validaton report |
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Full document | 3ivy_full_validation.pdf.gz | 822.1 KB | Display | |
Data in XML | 3ivy_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 3ivy_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/3ivy ftp://data.pdbj.org/pub/pdb/validation_reports/iv/3ivy | HTTPS FTP |
-Related structure data
Related structure data | 3iw0C 3iw1C 3iw2C 1cptS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48491.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Protein was produced in E.coli HMS174(DE3) (typically 15-20 L, grown in 2YT media) by IPTG (0.15 mM) induction in presence of the heme precursor delta aminolevulinic acid (delALA, 0.1 mM) at ...Details: Protein was produced in E.coli HMS174(DE3) (typically 15-20 L, grown in 2YT media) by IPTG (0.15 mM) induction in presence of the heme precursor delta aminolevulinic acid (delALA, 0.1 mM) at OD600 = 0.6, with temperature then reduced from 37 deg C to 23 deg C and culture continued for 24 hrs. Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: cyp125, MT3649, MTCY03C7.11, Rv3545c / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) References: UniProt: P63709, UniProt: P9WPP1*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen |
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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: 2.39 Å3/Da / Density % sol: 48.45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Crystallization was refined to two different conditions, both consisting of MgCl2 with 0.1 M HEPES (either pH 7.0 or 7.5) and 20% PEG 6000 or 25% PEG 3350, respectively. , VAPOR DIFFUSION, ...Details: Crystallization was refined to two different conditions, both consisting of MgCl2 with 0.1 M HEPES (either pH 7.0 or 7.5) and 20% PEG 6000 or 25% PEG 3350, respectively. , VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 1, 2007 Details: Single crystal monochromator and toroidal focusing mirror |
Radiation | Monochromator: Si(111) single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. all: 99798 / Num. obs: 99798 / % possible obs: 97.95 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.067 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.35→1.38 Å / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1CPT Resolution: 1.352→28.223 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 19.48 / 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 / Bsol: 71.998 Å2 / ksol: 0.38 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.352→28.223 Å
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Refine LS restraints |
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LS refinement shell |
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