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Yorodumi- PDB-1thg: 1.8 ANGSTROMS REFINED STRUCTURE OF THE LIPASE FROM GEOTRICHUM CANDIDUM -
+Open data
-Basic information
Entry | Database: PDB / ID: 1thg | ||||||||||||
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Title | 1.8 ANGSTROMS REFINED STRUCTURE OF THE LIPASE FROM GEOTRICHUM CANDIDUM | ||||||||||||
Components | Lipase 2 | ||||||||||||
Keywords | HYDROLASE(CARBOXYLIC ESTERASE) | ||||||||||||
Function / homology | Function and homology information triacylglycerol lipase / triglyceride lipase activity / lipid catabolic process / extracellular region Similarity search - Function | ||||||||||||
Biological species | Geotrichum candidum (yeast) | ||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||||||||
Authors | Schrag, J.D. / Cygler, M. | ||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: 1.8 A refined structure of the lipase from Geotrichum candidum. Authors: Schrag, J.D. / Cygler, M. #1: Journal: J.Biol.Chem. / Year: 1993 Title: Insights Into Interfacial Activation from an Open Structure of Candida Rugosa Lipase Authors: Grochulski, P. / Li, Y. / Schrag, J.D. / Bouthillier, F. / Smith, P. / Harrison, D. / Rubin, B. / Cygler, M. #2: Journal: J.Biol.Chem. / Year: 1992 Title: Pancreatic Lipases: Evolutionary Intermediates in a Positional Change of Catalytic Carboxylates? Authors: Schrag, J.D. / Winkler, F.K. / Cygler, M. #3: Journal: Nature / Year: 1991 Title: Ser-His-Glu Triad Forms the Catalytic Site of the Lipase from Geotrichum Candidum Authors: Schrag, J.D. / Li, Y. / Wu, S. / Cygler, M. #4: Journal: J.Mol.Biol. / Year: 1991 Title: Multiple Crystal Forms of Lipases from Geotrichum Candidum Authors: Schrag, J.D. / Li, Y. / Wu, S. / Cygler, M. #5: Journal: Nature / Year: 1990 Title: Structure of Human Pancreatic Lipase Authors: Winkler, F.K. / D'Arcy, A. / Hunziker, W. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1thg.cif.gz | 123.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1thg.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 1thg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/1thg ftp://data.pdbj.org/pub/pdb/validation_reports/th/1thg | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUE 403 IS A CIS PROLINE. |
-Components
#1: Protein | Mass: 59727.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geotrichum candidum (yeast) / Strain: ATCC 34614 / Gene: LIP2 / References: UniProt: P22394, triacylglycerol lipase |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Sugar | ChemComp-NAG / |
#4: Sugar | ChemComp-NDG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.56 % | |||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 48512 / % possible obs: 96.6 % / Num. measured all: 188971 / Rmerge(I) obs: 0.0393 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.157 / Rfactor obs: 0.157 / Highest resolution: 1.8 Å Details: HELICES FL1 AND FL2 FORM A FLAP COVERING THE ACTIVE SITE. THE FLAP COMPRISES RESIDUES 61 - 105. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 43230 / σ(I): 2 / Rfactor obs: 0.157 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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