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Yorodumi- PDB-6or3: Structure of an Acyl Intermediate of Thermomyces Lanuginosa Lipas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6or3 | ||||||
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Title | Structure of an Acyl Intermediate of Thermomyces Lanuginosa Lipase With Palmitic Acid in an Orthorhombic Crystal | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE / product complex / acyl intermediate / dimer / palmitic acid / LIPID BINDING PROTEIN | ||||||
Function / homology | Function and homology information triacylglycerol lipase / triglyceride lipase activity / lipid catabolic process Similarity search - Function | ||||||
Biological species | Thermomyces lanuginosus (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | McPherson, A. | ||||||
Citation | Journal: Current Enzyme Inhibition / Year: 2020 Title: The crystal Structures of Thermomyces (Humicola) lanuginosa lipase in complex with enzymatic reactants Authors: McPherson, A. / Larson, S.B. / Kalasky, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6or3.cif.gz | 175.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6or3.ent.gz | 141.4 KB | Display | PDB format |
PDBx/mmJSON format | 6or3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/6or3 ftp://data.pdbj.org/pub/pdb/validation_reports/or/6or3 | HTTPS FTP |
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-Related structure data
Related structure data | 6xokC 6xrvC 6xs3C 1tibS 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31836.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) / References: UniProt: O59952, triacylglycerol lipase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-PLM / |
#4: Sugar | ChemComp-NAG / |
#5: 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: 2.17 Å3/Da / Density % sol: 40 % / Description: orthorhombic prisms |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Using filtered culture media with active fungal cells as the stock protein solution, about 30 mg/ml. Sitting drop equal amounts of the protein stock and the reservoir which was 20% PEG 335 ...Details: Using filtered culture media with active fungal cells as the stock protein solution, about 30 mg/ml. Sitting drop equal amounts of the protein stock and the reservoir which was 20% PEG 335 buffered with 0.10 M MES at pH 6.5 PH range: 6.0 - 7.5 |
-Data collection
Diffraction | Mean temperature: 173 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Mar 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→60.8 Å / Num. obs: 46198 / % possible obs: 99.9 % / Redundancy: 62.8 % / Biso Wilson estimate: 23 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.334 / Rrim(I) all: 0.337 / Rsym value: 0.32 / Net I/av σ(I): 10.4 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 38.7 % / Rmerge(I) obs: 3.6 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2213 / CC1/2: 0.294 / Rrim(I) all: 3.7 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TIB Resolution: 1.45→60 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.963 / SU B: 6.25 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.072 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.572 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→60 Å
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Refine LS restraints |
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