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- PDB-1gz7: Crystal structure of the closed state of lipase 2 from Candida rugosa -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gz7 | |||||||||
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Title | Crystal structure of the closed state of lipase 2 from Candida rugosa | |||||||||
![]() | LIPASE 2 | |||||||||
![]() | HYDROLASE / CARBOXYLIC ESTERASE / GLYCOPROTEIN. | |||||||||
Function / homology | ![]() triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mancheno, J.M. / Hermoso, J.A. | |||||||||
![]() | ![]() Title: Structural Insights Into the Lipase/Esterase Behavior in the Candida Rugosa Lipases Family: Crystal Structure of the Lipase 2 Isoenzyme at 1.97A Resolution Authors: Mancheno, J.M. / Pernas, M.A. / Martinez, M.J. / Ochoa, B. / Rua, M.L. / Hermoso, J.A. #1: Journal: Methods Enzymol. / Year: 1997 Title: Cloning, Sequencing, and Expression of Candida Rugosa Lipases Authors: Alberghina, L. / Lotti, M. #2: Journal: Nature / Year: 1989 Title: The Codon Cug is Read as Serine in an Asporogenic Yeast Candida Cylindracea Authors: Kawaguchi, Y. / Honda, H. / Taniguchi-Morimura, J. / Iwasaki, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 432.3 KB | Display | ![]() |
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PDB format | ![]() | 354.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 639.7 KB | Display | ![]() |
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Full document | ![]() | 674.8 KB | Display | |
Data in XML | ![]() | 45.5 KB | Display | |
Data in CIF | ![]() | 76.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1trhS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 57509.344 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #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: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: 15% (W/V) PEG 4000, SODIUM ACETATE 0.1M, PH 5.0 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / pH: 5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: May 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.004 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→37.11 Å / Num. obs: 152503 / % possible obs: 94.6 % / Redundancy: 2 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 1.97→2.08 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 2.2 / % possible all: 76.5 |
Reflection | *PLUS Highest resolution: 1.97 Å / Num. measured all: 299637 / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 76.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TRH Resolution: 1.97→11.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 935285.74 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE ELECTRON DENSITY CORRESPONDING TO RESIDUES 78 AND 79 IS NOT CONSISTENT WITH THE SEQUENCE DESCRIBED FOR LIPASE2 (ARG-HIS), BUT WITH LEU-ASP, PRECISELY THE SEQUENCE DESCRIBED FOR LIPASE 1 AND LIPASE 3.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.0866 Å2 / ksol: 0.42525 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.97→11.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.09 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 12 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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