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Yorodumi- PDB-6xs3: X-ray structure of the monoclinic crystal form at 2.48 A resoluti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xs3 | ||||||
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Title | X-ray structure of the monoclinic crystal form at 2.48 A resolution of lipase from Thermomyces (Humicola) lanuginosa at 298 K | ||||||
Components | Lipase | ||||||
Keywords | LIPID BINDING PROTEIN / substrate complex / diacylglycerol / covalent intermediate / interfacial activation | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.48 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 | 6xs3.cif.gz | 597.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xs3.ent.gz | 501.3 KB | Display | PDB format |
PDBx/mmJSON format | 6xs3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/6xs3 ftp://data.pdbj.org/pub/pdb/validation_reports/xs/6xs3 | HTTPS FTP |
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-Related structure data
Related structure data | 6or3C 6xokC 6xrvC 4ea6S 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
-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: Aspergillus aculeatinus (mold) / 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: cube shaped blocks |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: CXrystals were grown by sitting drop in Cryschem plates using 0.6 ml reservoirs of 20% PEG 3350 in 0.1M MES buffer. The drops were 6 ul composed of equal amounts of protein at 30 mg/ml in ...Details: CXrystals were grown by sitting drop in Cryschem plates using 0.6 ml reservoirs of 20% PEG 3350 in 0.1M MES buffer. The drops were 6 ul composed of equal amounts of protein at 30 mg/ml in water with the reservoir solution. Temperature was 298 K and crystals appeared after about two weeks PH range: 6.0 - 7.0 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419 Å |
Detector | Type: OXFORD RUBY CCD / Detector: CCD / Date: Jun 20, 2017 |
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→75 Å / Num. obs: 81074 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 26 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.292 / Rpim(I) all: 0.102 / Rrim(I) all: 0.327 / Rsym value: 0.287 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.48→2.55 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: 0.62 / Rrim(I) all: 1.3 / Rsym value: 1.01 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EA6 Resolution: 2.48→51.27 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.19 / Stereochemistry target values: ML Details: Structure was refined to convergence with REFMAC5 in CCP4, then five runs through PHENIX REFINE using isotropic B values and no TLS.
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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 max: 164 Å2 / Biso mean: 36.1154 Å2 / Biso min: 9.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.48→51.27 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22
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