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Yorodumi- PDB-6xrv: X-ray structure of the monoclinic crystal form at 1.43 A resoluti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xrv | ||||||
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Title | X-ray structure of the monoclinic crystal form at 1.43 A resolution of lipase from Thermomyces (Humicola) lanuginosa at 173 K | ||||||
Components | Lipase | ||||||
Keywords | LIPID BINDING PROTEIN / substrate complex / diacylglycerol / covalent intermediate / interfacial activation | ||||||
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: 1.43 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 | 6xrv.cif.gz | 980 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xrv.ent.gz | 833 KB | Display | PDB format |
PDBx/mmJSON format | 6xrv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/6xrv ftp://data.pdbj.org/pub/pdb/validation_reports/xr/6xrv | HTTPS FTP |
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-Related structure data
Related structure data | 6or3C 6xokC 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
-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 #3: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 1645 molecules
#2: Chemical | ChemComp-OCA / #4: Chemical | ChemComp-LTV / #5: Chemical | ChemComp-PO4 / #6: Chemical | ChemComp-CA / #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: 2.23 Å3/Da / Density % sol: 44.8 % / Description: cube like blocks |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Crystals grown by sitting drop with 0.6 ul reservoirs of 20% PEG 3350 in 0.1 M MES buffer at pH 6.5. Drops of 8 ul composed of equal amounts of the protein at 30.0 mg/ml in water with the ...Details: Crystals grown by sitting drop with 0.6 ul reservoirs of 20% PEG 3350 in 0.1 M MES buffer at pH 6.5. Drops of 8 ul composed of equal amounts of the protein at 30.0 mg/ml in water with the reservoir solution. Room temperature throughout, crystals grew in about a month PH range: 6.0 - 7.0 |
-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 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→77 Å / Num. obs: 307462 / % possible obs: 99.7 % / Redundancy: 19.2 % / Biso Wilson estimate: 22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.036 / Rrim(I) all: 0.163 / Rsym value: 0.156 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.43→1.45 Å / Redundancy: 13.3 % / Rmerge(I) obs: 5.69 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 15076 / CC1/2: 0.26 / Rpim(I) all: 1.66 / Rrim(I) all: 6.1 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TIB Resolution: 1.43→77 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.66 / Stereochemistry target values: ML Details: Refined to convergence in REFMAC then subjected to further rebuilding in COOT and an additional 15 runs in REFINE from PHENIX. Anisotropic B values, 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: 74.3 Å2 / Biso mean: 29.7343 Å2 / Biso min: 8.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.43→77 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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