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Yorodumi- PDB-5lip: PSEUDOMONAS LIPASE COMPLEXED WITH RC-(RP, SP)-1,2-DIOCTYLCARBAMOY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lip | ||||||
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Title | PSEUDOMONAS LIPASE COMPLEXED WITH RC-(RP, SP)-1,2-DIOCTYLCARBAMOYLGLYCERO-3-O-OCTYLPHOSPHONATE | ||||||
Components | TRIACYL-GLYCEROL HYDROLASE | ||||||
Keywords | LIPASE / PSEUDOMONADACEAE / COVALENT INTERMEDIATE / TRIGLYCERIDE ANALOGUE / ENANTIOSELECTIVITY | ||||||
Function / homology | Function and homology information triacylglycerol lipase / triglyceride lipase activity / lipid catabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Burkholderia cepacia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Lang, D.A. / Dijkstra, B.W. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 1998 Title: Structural basis of the chiral selectivity of Pseudomonas cepacia lipase Authors: Lang, D.A. / Mannesse, M.L.M. / De Haas, G. / Verheij, H.M. / Dijkstra, B.W. #1: Journal: Structure / Year: 1997 Title: The Open Conformation of a Pseudomonas Lipase Authors: Schrag, J.D. / Li, Y. / Cygler, M. / Lang, D. / Burgdorf, T. / Hecht, H.J. / Schmid, R. / Schomburg, D. / Rydel, T.J. / Oliver, J.D. / Strickland, L.C. / Dunaway, C.M. / Larson, S.B. / Day, J. / McPherson, A. #2: Journal: J.Bacteriol. / Year: 1991 Title: Extracellular Lipase of Pseudomonas Sp. Strain Atcc 21808: Purification, Characterization, Crystallization, and Preliminary X-Ray Diffraction Data Authors: Kordel, M. / Hofmann, B. / Schomburg, D. / Schmid, R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lip.cif.gz | 67 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lip.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 5lip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/5lip ftp://data.pdbj.org/pub/pdb/validation_reports/li/5lip | HTTPS FTP |
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-Related structure data
Related structure data | 4lipC 3lipS 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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Unit cell |
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-Components
#1: Protein | Mass: 33150.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cepacia (bacteria) / Cellular location: EXTRACELLULARGlossary of biology / Plasmid: PHES12 / Production host: Pseudomonas sp. (bacteria) / Strain (production host): 21808 / References: UniProt: P22088, triacylglycerol lipase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-OCP / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | THE STARTING MATERIAL FOR THE INHIBITOR WAS RC-(RP,SP)-1,2- DIOCTYLCARBAMOYL-GLYCERO-3-O-P- ...THE STARTING MATERIAL FOR THE INHIBITOR WAS RC-(RP,SP)-1,2- DIOCTYLCAR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4 Details: 14 % ISOPROPANOL, 0.020 M CACL2, 0.1 M ACETATE, PH 4, pH 4.0 | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12 ℃ / pH: 9 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. obs: 6515 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.092 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.9→2.95 Å / Rsym value: 0.158 / % possible all: 87.2 |
Reflection | *PLUS Num. measured all: 22335 / Rmerge(I) obs: 0.092 |
Reflection shell | *PLUS Rmerge(I) obs: 0.158 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3LIP Resolution: 2.9→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 0 Details: THE CIS-PEPTIDE BOND VISIBLE IN THE HIGH RESOLUTION STRUCTURES COULD NOT BE KEPT AT 2.9 ANG.
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Displacement parameters | Biso mean: 7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.03 Å / Total num. of bins used: 8 /
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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