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Yorodumi- PDB-2x5w: X-ray structure of Mycobacterium tuberculosis cytochrome P450 CYP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x5w | ||||||
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Title | X-ray structure of Mycobacterium tuberculosis cytochrome P450 CYP125 in complex with substrate cholest-4-en-3-one | ||||||
Components | PUTATIVE CYTOCHROME P450 125 | ||||||
Keywords | OXIDOREDUCTASE / CHOLESTEROL DEGRADATION / METAL-BINDING | ||||||
Function / homology | Function and homology information cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] / cholest-4-en-3-one 26-monooxygenase activity / biological process involved in interaction with host / 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: 1.58 Å | ||||||
Authors | Ouellet, H. / Guan, S. / Johnston, J.B. / Chow, E.D. / Kells, P.M. / Burlingame, A.L. / Cox, J.S. / Podust, L.M. / Ortiz de Montellano, P.R. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2010 Title: Mycobacterium Tuberculosis Cyp125A1, a Steroid C27 Monooxygenase that Detoxifies Intracellularly Generated Cholest-4-En-3-One. Authors: Ouellet, H. / Guan, S. / Johnston, J.B. / Chow, E.D. / Kells, P.M. / Burlingame, A.L. / Cox, J.S. / Podust, L.M. / Ortiz de Montellano, P.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x5w.cif.gz | 202 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x5w.ent.gz | 160.1 KB | Display | PDB format |
PDBx/mmJSON format | 2x5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/2x5w ftp://data.pdbj.org/pub/pdb/validation_reports/x5/2x5w | HTTPS FTP |
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-Related structure data
Related structure data | 3ivyS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49451.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PCWORI / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): HMS174 References: UniProt: P63709, UniProt: P9WPP1*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen |
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-Non-polymers , 5 types, 442 molecules
#2: Chemical | ChemComp-SO4 / |
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#3: Chemical | ChemComp-K2B / ( |
#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-HEM / |
#6: 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: 2.3 Å3/Da / Density % sol: 46.6 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 5.5 Details: 0.2 M AMMONIUM SULPHATE, 0.1 M BIS- TRIS, PH 5.5, 25% PEG 3350, 4 DEGREE C. |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 15, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1159 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→75.98 Å / Num. obs: 61386 / % possible obs: 99.3 % / Observed criterion σ(I): 1.5 / Redundancy: 4.4 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.58→1.67 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.6 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IVY Resolution: 1.58→79.59 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.286 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.081 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.84 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→79.59 Å
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Refine LS restraints |
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