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Yorodumi- PDB-6osz: High Resolution Structure of the Monoclinic Form of Thermomyces L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6osz | ||||||
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Title | High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE / fatty acids / diacylglycerol / 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: 1.43 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 | 6osz.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6osz.ent.gz | 847.2 KB | Display | PDB format |
PDBx/mmJSON format | 6osz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6osz_validation.pdf.gz | 4.9 MB | Display | wwPDB validaton report |
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Full document | 6osz_full_validation.pdf.gz | 5 MB | Display | |
Data in XML | 6osz_validation.xml.gz | 82.7 KB | Display | |
Data in CIF | 6osz_validation.cif.gz | 118.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/6osz ftp://data.pdbj.org/pub/pdb/validation_reports/os/6osz | HTTPS FTP |
-Related structure data
Related structure data | 6o8vC 6o9fC 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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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: Thermomyces lanuginosus (fungus) / References: UniProt: O59952, triacylglycerol lipase #3: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 1757 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: blocks of about equal dimensions, about .30 mm edge lengths |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Sitting drop vapor diffusion at room temperature in 10 ul drops. Drops composed of equal amounts of stock protein solution, which was approximately 30 mg/ml lipase in the filtered culture ...Details: Sitting drop vapor diffusion at room temperature in 10 ul drops. Drops composed of equal amounts of stock protein solution, which was approximately 30 mg/ml lipase in the filtered culture media, and the reservoir solution. The latter was 20% PEG 3350 buffered at pH 6.5 with 0.10 M MES 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 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 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→77 Å / Num. obs: 307462 / % possible obs: 99.7 % / Redundancy: 19.5 % / Biso Wilson estimate: 21.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.036 / Rrim(I) all: 0.163 / Rsym value: 0.153 / Net I/av σ(I): 9.1 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.43→1.45 Å / Redundancy: 13.3 % / Rmerge(I) obs: 5.7 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 15076 / CC1/2: 0.264 / Rpim(I) all: 1.66 / Rrim(I) all: 6.1 / Rsym value: 5.6 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TIB Resolution: 1.43→76.69 Å / SU ML: 0.1965 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.3727 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: 28.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→76.69 Å
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Refine LS restraints |
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LS refinement shell |
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