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- PDB-4lip: PSEUDOMONAS LIPASE COMPLEXED WITH RC-(RP, SP)-DIBUTYLCARBAMOYLGLY... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4lip | ||||||
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Title | PSEUDOMONAS LIPASE COMPLEXED WITH RC-(RP, SP)-DIBUTYLCARBAMOYLGLYCERO-3-O-BUTYLPHOSPHONATE | ||||||
![]() | TRIACYL-GLYCEROL-HYDROLASE | ||||||
![]() | LIPASE / HYDROLASE / PSEUDOMONADACEAE / COVALENT INTERMEDIATE / TRIGLYCERIDE ANALOGUE / ENANTIOSELECTIVITY | ||||||
Function / homology | ![]() triacylglycerol lipase / triglyceride lipase activity / lipid catabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lang, D.A. / Dijkstra, B.W. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.4 KB | Display | ![]() |
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PDB format | ![]() | 107.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 387.4 KB | Display | ![]() |
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Full document | ![]() | 390.7 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lipC ![]() 3lipS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9998, 0.0208, 0.001), Vector: |
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Components
#1: Protein | Mass: 33150.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | THE STARTING MATERIAL FOR THE INHIBITOR WAS RC-(RP,SP)-1,2-DIBUTYLCARBAMOYL-GLYCERO-3-O-P- ...THE STARTING MATERIAL FOR THE INHIBITOR WAS RC-(RP,SP)-1,2-DIBUTYLCAR | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: 20 % MPD, 100 MM CACL2, 0.1 M TRIS/HCL, PH 8.5 | ||||||||||||||||||||||||||||||||||||
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: 90 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 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: 1.75→30 Å / Num. obs: 56937 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 2.46 % / Rsym value: 0.031 / Net I/σ(I): 45.8 |
Reflection shell | Resolution: 1.75→1.83 Å / Mean I/σ(I) obs: 26.2 / Rsym value: 0.059 / % possible all: 93.9 |
Reflection | *PLUS Num. measured all: 140279 / Rmerge(I) obs: 0.031 |
Reflection shell | *PLUS Rmerge(I) obs: 0.059 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3LIP Resolution: 1.75→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 0 Details: THE STRUCTURE WAS INITIALLY REFINED WITH STRICT NON-CRYSTALLOGRAPHIC SYMMETRY, AND THEN WITH TIGHTLY RESTRAINED NON-CRYSTALLOGRAPHIC SYMMETRY FOR ALL PARTS OF THE MOLECULE EXCEPT RESIDUES 16 ...Details: THE STRUCTURE WAS INITIALLY REFINED WITH STRICT NON-CRYSTALLOGRAPHIC SYMMETRY, AND THEN WITH TIGHTLY RESTRAINED NON-CRYSTALLOGRAPHIC SYMMETRY FOR ALL PARTS OF THE MOLECULE EXCEPT RESIDUES 16 - 28, 127 - 159, AND 218 - 224. THE CHAINS ARE NAMED D AND E, WITH MOLECULE D AS THE REFERENCE FOR SECONDARY STRUCTURE DEFINITION. DEVIATIONS FROM NON-CRYSTALLOGRAPHIC SYMMETRY CORRESPOND TO THOSE PARTS OF THE PROTEIN EXCLUDED FROM THE NCS-RESTRAINT.
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Displacement parameters | Biso mean: 8.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: PARTIAL RESTRAINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.75→1.83 Å / Total num. of bins used: 8 /
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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