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Yorodumi- PDB-5onc: Catabolism of the Cholesterol Side Chain in Mycobacterium tubercu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5onc | |||||||||||||||
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Title | Catabolism of the Cholesterol Side Chain in Mycobacterium tuberculosis is Controlled by a Redox-Sensitive Thiol Switch | |||||||||||||||
Components | Steroid 3-ketoacyl-CoA thiolase | |||||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / Oxidative Stress / Cholesterol Metabolism / Lipid degradation / Steroid metabolism / Mycobacterium tuberculosis | |||||||||||||||
Function / homology | Function and homology information acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / phenylacetate catabolic process / fatty acid beta-oxidation / cholesterol catabolic process / identical protein binding Similarity search - Function | |||||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | |||||||||||||||
Authors | Schaefer, C. / Kuper, J. / Sampson, N.S. / Kisker, C. | |||||||||||||||
Funding support | United States, Germany, 4items
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Citation | Journal: ACS Infect Dis / Year: 2017 Title: Catabolism of the Cholesterol Side Chain in Mycobacterium tuberculosis Is Controlled by a Redox-Sensitive Thiol Switch. Authors: Lu, R. / Schaefer, C.M. / Nesbitt, N.M. / Kuper, J. / Kisker, C. / Sampson, N.S. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5onc.cif.gz | 290 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5onc.ent.gz | 236.5 KB | Display | PDB format |
PDBx/mmJSON format | 5onc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5onc_validation.pdf.gz | 302.5 KB | Display | wwPDB validaton report |
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Full document | 5onc_full_validation.pdf.gz | 316.4 KB | Display | |
Data in XML | 5onc_validation.xml.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/5onc ftp://data.pdbj.org/pub/pdb/validation_reports/on/5onc | HTTPS FTP |
-Related structure data
Related structure data | 4ubwS 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 1 - 391 / Label seq-ID: 9 - 399
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-Components
#1: Protein | Mass: 42346.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: fadA5, LH57_19345, Rv3546 / Plasmid: pSD31 / Production host: Mycobacterium smegmatis (bacteria) / References: UniProt: I6XHI4, acetyl-CoA C-acyltransferase #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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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: 2.54 Å3/Da / Density % sol: 51.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M citrate, pH 5.5, 0.7 M (NH4)2HPO4, 0.3 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 9, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→46.17 Å / Num. obs: 46018 / % possible obs: 100 % / Redundancy: 9.8 % / Rsym value: 0.1 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.19→2.26 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3897 / CC1/2: 0.756 / Rsym value: 0.96 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UBW Resolution: 2.19→46.17 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.613 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.984 Å2
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Refinement step | Cycle: 1 / Resolution: 2.19→46.17 Å
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Refine LS restraints |
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