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Yorodumi- PDB-2yoo: Cholest-4-en-3-one bound structure of CYP142 from Mycobacterium s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yoo | ||||||
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Title | Cholest-4-en-3-one bound structure of CYP142 from Mycobacterium smegmatis | ||||||
Components | P450 HEME-THIOLATE PROTEIN | ||||||
Keywords | OXIDOREDUCTASE / CHOLESTEROL METABOLISM | ||||||
Function / homology | Function and homology information cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] / cholesterol catabolic process / 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 smegmatis str. MC2 155 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Garcia-Fernandez, E. / Frank, D.J. / Galan, B. / Kells, P.M. / Podust, L.M. / Garcia, J.L. / Ortiz de Montellano, P.R. | ||||||
Citation | Journal: Environ.Microbiol. / Year: 2013 Title: A Highly Conserved Mycobacterial Cholesterol Catabolic Pathway. Authors: Garcia-Fernandez, E. / Frank, D.J. / Galan, B. / Kells, P.M. / Podust, L.M. / Garcia, J.L. / 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 | 2yoo.cif.gz | 360.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yoo.ent.gz | 293.2 KB | Display | PDB format |
PDBx/mmJSON format | 2yoo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/2yoo ftp://data.pdbj.org/pub/pdb/validation_reports/yo/2yoo | HTTPS FTP |
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-Related structure data
Related structure data | 3zbyC 4apyC 4bb8 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 45780.012 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: 6XHIS TAG ENGINEERED AT C-TERMINUS Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria) Plasmid: PCW / Production host: Escherichia coli (E. coli) / References: UniProt: A0R4Q6 #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-K2B / ( #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Nonpolymer details | PROTOPORPHYRIN IX CONTAINING FE (HEM): THIOLATE BOND TO CYS 343 (8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE ...PROTOPORPH | Sequence details | 6XHIS TAG ENGINEERED | |
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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: 2.07 Å3/Da / Density % sol: 40.6 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 24% PEG 3350, 0.2 M MGCL2, 0.1 M MES, PH 6.0 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→106.21 Å / Num. obs: 156144 / % possible obs: 93.5 % / Observed criterion σ(I): 1.5 / Redundancy: 2.2 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.69→1.78 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.5 / % possible all: 65.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BB8 4bb8 Resolution: 1.69→126.53 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.354 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.121 / 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: 15.957 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→126.53 Å
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Refine LS restraints |
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