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Yorodumi- PDB-6o8v: The structure of lipase from Thermomyces Lanuginosa in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o8v | ||||||
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Title | The structure of lipase from Thermomyces Lanuginosa in complex with 1,3 diacylglycerol: Rhombohedral crystal form | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE / trimer / esterase / lipids / lipase / substrate complex / catalysis / acyl intermediate / LIPID BINDING PROTEIN | ||||||
Function / homology | Function and homology information triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process Similarity search - Function | ||||||
Biological species | Thermomyces lanuginosus (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | McPherson, A. | ||||||
Funding support | 1items
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Citation | Journal: Curr Enzym Inhib / Year: 2020 Title: The Crystal Structures of Thermomyces (Humicola) Lanuginosa Lipase in Complex with Enzymatic Reactants Authors: McPherson , A. / Larson , B.S. / Kalasky , A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o8v.cif.gz | 219 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o8v.ent.gz | 146.3 KB | Display | PDB format |
PDBx/mmJSON format | 6o8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6o8v_validation.pdf.gz | 980.2 KB | Display | wwPDB validaton report |
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Full document | 6o8v_full_validation.pdf.gz | 985.6 KB | Display | |
Data in XML | 6o8v_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 6o8v_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/6o8v ftp://data.pdbj.org/pub/pdb/validation_reports/o8/6o8v | HTTPS FTP |
-Related structure data
Related structure data | 6o9fC 6oszC 1tibS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 31836.459 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermomyces lanuginosus (fungus) / Gene: LIP / Production host: Thermoactinomyces vulgaris (bacteria) / References: UniProt: O59952, triacylglycerol lipase |
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#2: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 412 molecules
#3: Chemical | ChemComp-PG4 / | ||||
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#4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-LTV / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.13 Å3/Da / Density % sol: 42.23 % / Description: thin needles of indeterminate cross section |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: From a filtered, crude nutrient broth containing 30 - 50 mg/ml lipase plus 25% PEG 3350 plus 0.10 M MES buffer at room temperature PH range: 6.0 - 7.5 |
-Data collection
Diffraction | Mean temperature: 173 K / Ambient temp details: flash frozen in cryostream / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.03 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→100 Å / Num. obs: 58358 / % possible obs: 88 % / Redundancy: 31 % / Biso Wilson estimate: 13.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.01 / Rrim(I) all: 0.05 / Rsym value: 0.046 / Net I/av σ(I): 42.7 / Net I/σ(I): 42.7 |
Reflection shell | Resolution: 1.3→1.33 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 463 / CC1/2: 0.81 / Rpim(I) all: 0.205 / Rrim(I) all: 0.461 / Rsym value: 0.34 / % possible all: 14.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1tib Resolution: 1.3→80.52 Å / SU ML: 0.0934 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 13.2256 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→80.52 Å
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Refine LS restraints |
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LS refinement shell |
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