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Yorodumi- PDB-3cxz: Crystal structure of cytochrome P450 CYP121 R386L mutant from M. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cxz | ||||||
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Title | Crystal structure of cytochrome P450 CYP121 R386L mutant from M. tuberculosis | ||||||
Components | Cytochrome P450 121 | ||||||
Keywords | OXIDOREDUCTASE / cytochrome P450 / CYP121 / Mycobacterium tuberculosis / Heme / Iron / Metal-binding / Monooxygenase | ||||||
Function / homology | Function and homology information mycocyclosin synthase / oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water / cyclase activity / carbon monoxide binding / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / monooxygenase activity / oxidoreductase activity / iron ion binding ...mycocyclosin synthase / oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water / cyclase activity / carbon monoxide binding / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / monooxygenase activity / oxidoreductase activity / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.08 Å | ||||||
Authors | Leys, D. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Characterization of active site structure of cytochrome P450 CYP121 Authors: McLean, K.J. / Carrol, P. / Lewis, D.G. / Dunford, A.J. / Seward, H.E. / Neeli, R. / Cole, S.T. / Leys, D. / Parish, T. / 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 | 3cxz.cif.gz | 206.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cxz.ent.gz | 162.7 KB | Display | PDB format |
PDBx/mmJSON format | 3cxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/3cxz ftp://data.pdbj.org/pub/pdb/validation_reports/cx/3cxz | HTTPS FTP |
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-Related structure data
Related structure data | 1n40S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Details | monomer in the AU, oligomeric organisation in solvent is unclear |
-Components
#1: Protein | Mass: 43261.824 Da / Num. of mol.: 1 / Mutation: R386L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: cyp121 / Production host: Escherichia coli (E. coli) References: UniProt: P0A514, UniProt: P9WPP7*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen | ||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.47 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2 M ammonium sulphate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.96 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 5, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→20 Å / Num. all: 174111 / Num. obs: 174111 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.087 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1N40 Resolution: 1.08→19.93 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.768 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.028 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.234 Å2
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Refinement step | Cycle: LAST / Resolution: 1.08→19.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.08→1.108 Å / Total num. of bins used: 20
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