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Yorodumi- PDB-7cog: Cholesterol esterase from Burkholderia stabilis (monoclinic cryst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cog | ||||||
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Title | Cholesterol esterase from Burkholderia stabilis (monoclinic crystal form) | ||||||
Components | Alpha/beta hydrolaseAlpha/beta hydrolase superfamily | ||||||
Keywords | HYDROLASE / cholesterol esterase / lipase / Burkholderia stabilis | ||||||
Function / homology | alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Alpha/beta hydrolase Function and homology information | ||||||
Biological species | Burkholderia stabilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å | ||||||
Authors | Yasutake, Y. / Tamura, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2021 Title: Bacterial triacylglycerol lipase is a potential cholesterol esterase: Identification of a key determinant for sterol-binding specificity. Authors: Yasutake, Y. / Konishi, K. / Muramatsu, S. / Yoshida, K. / Aburatani, S. / Sakasegawa, S.I. / Tamura, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cog.cif.gz | 236.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cog.ent.gz | 189.6 KB | Display | PDB format |
PDBx/mmJSON format | 7cog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/7cog ftp://data.pdbj.org/pub/pdb/validation_reports/co/7cog | HTTPS FTP |
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-Related structure data
Related structure data | 7cofC 1ys1S 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: 33235.844 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: WP_096474789.1 / Source: (natural) Burkholderia stabilis (bacteria) / References: UniProt: A0A1Y1BQV9 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.31 Å3/Da / Density % sol: 46.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: sodium citrate, PEG4000, 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.098→50 Å / Num. obs: 71702 / % possible obs: 99.5 % / Redundancy: 3.36 % / Rrim(I) all: 0.122 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.098→2.23 Å / Mean I/σ(I) obs: 2.31 / Num. unique obs: 11384 / Rrim(I) all: 0.552 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YS1 Resolution: 2.098→46.497 Å / Cross valid method: THROUGHOUT / σ(F): 2.2 / Phase error: 42.52 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.098→46.497 Å
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Refine LS restraints |
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LS refinement shell |
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