+Open data
-Basic information
Entry | Database: PDB / ID: 3zby | |||||||||
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Title | Ligand-free structure of CYP142 from Mycobacterium smegmatis | |||||||||
Components | P450 HEME-THIOLATE PROTEIN | |||||||||
Keywords | OXIDOREDUCTASE / CYP142 / CHOLESTEROL METABOLISM | |||||||||
Function / homology | Function and homology information cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] / 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 smegmatis str. MC2 155 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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 | 3zby.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3zby.ent.gz | 915.9 KB | Display | PDB format |
PDBx/mmJSON format | 3zby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zby_validation.pdf.gz | 5.5 MB | Display | wwPDB validaton report |
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Full document | 3zby_full_validation.pdf.gz | 5.6 MB | Display | |
Data in XML | 3zby_validation.xml.gz | 128.1 KB | Display | |
Data in CIF | 3zby_validation.cif.gz | 186.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/3zby ftp://data.pdbj.org/pub/pdb/validation_reports/zb/3zby | HTTPS FTP |
-Related structure data
Related structure data | 2yooC 4apyC 2xkrS 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 on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 12 molecules ABCDEF
#1: Protein | Mass: 45780.012 Da / Num. of mol.: 6 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 DH5[alpha] (bacteria) / References: UniProt: A0R4Q6 #2: Polysaccharide | Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin |
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-Non-polymers , 4 types, 2666 molecules
#3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | 1,2-ETHANEDIOL (EDO): CRYO-PROTECTANT PROTOPORPHYRIN IX CONTAINING FE (HEM): FE THIOLATE BOND TO ...1,2-ETHANEDIOL |
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Sequence details | 6XHIS TAG ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.6 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 1.4 M AMMONIUM SULPHATE, 0.1 M BIS TRIS, PH 7.5; 0.1 M LICL |
-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: MARRESEARCH / 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: 1.92→81.44 Å / Num. obs: 287620 / % possible obs: 94.5 % / Observed criterion σ(I): 1.5 / Redundancy: 2.7 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.92→2.02 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.5 / % possible all: 74.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XKR Resolution: 1.93→266.44 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.259 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.133 / 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: 25.564 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→266.44 Å
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Refine LS restraints |
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