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Yorodumi- PDB-6o9f: The structure of Thermomyces Lanuginosa lipase in complex with 1,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o9f | ||||||
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Title | The structure of Thermomyces Lanuginosa lipase in complex with 1,3 diacylglycerol in a monoclinic crystal form | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE / lipids / triglycerides / catalytic triad / monolayer / acyl intermediate / trimer / NCS / 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 / MOLECULAR REPLACEMENT / Resolution: 2.48 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 | 6o9f.cif.gz | 738.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o9f.ent.gz | 500.9 KB | Display | PDB format |
PDBx/mmJSON format | 6o9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/6o9f ftp://data.pdbj.org/pub/pdb/validation_reports/o9/6o9f | HTTPS FTP |
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-Related structure data
Related structure data | 6o8vC 6oszC 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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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 12 molecules ABCEDF
#1: Protein | Mass: 31836.459 Da / Num. of mol.: 6 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 #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 453 molecules
#2: Chemical | ChemComp-OCA / #3: Chemical | ChemComp-CA / #5: Chemical | ChemComp-LTV / #6: Chemical | ChemComp-PO4 / #7: Water | ChemComp-HOH / | |
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-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: 2.32 Å3/Da / Density % sol: 46.91 % Description: Thick equidimensional blocks 0.25 to 0.50 mm edge lengths |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein source was a filtered fungal culture medium at about 50 mg/ml. This was combined in 8 ul drops with equal amounts of 25% PEG 3350 buffered at pH 6.5 with 0.10 M MES and crystallized ...Details: Protein source was a filtered fungal culture medium at about 50 mg/ml. This was combined in 8 ul drops with equal amounts of 25% PEG 3350 buffered at pH 6.5 with 0.10 M MES and crystallized at room temperature by sitting drops in Cryschem plates PH range: 6.0 - 7.5 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5419 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: May 15, 2016 |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→80 Å / Num. obs: 81074 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 27.29 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.292 / Rpim(I) all: 0.102 / Rrim(I) all: 0.327 / Rsym value: 0.245 / Net I/av σ(I): 7.1 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.48→2.52 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4362 / CC1/2: 0.18 / Rpim(I) all: 0.623 / Rrim(I) all: 1.3 / Rsym value: 0.85 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→51.27 Å / SU ML: 0.3209 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.021 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: 32.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.48→51.27 Å
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Refine LS restraints |
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LS refinement shell |
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