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Open data
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Basic information
Entry | Database: PDB / ID: 7r25 | |||||||||
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Title | Bacillus pumilus Lipase A | |||||||||
![]() | Lipase![]() | |||||||||
![]() | ![]() ![]() ![]() | |||||||||
Function / homology | Lipase EstA/Esterase EstB / Lipase (class 2) / lipid catabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lund, B.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and Mechanism of a Cold-Adapted Bacterial Lipase Authors: Lund, B.A. / Svalberg, L. / Purg, M. / Chukwu, G. / Widersten, M. / Isaksen, G.V. / Brandsdal, B.O. / Aqvist, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.8 KB | Display | ![]() |
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PDB format | ![]() | 103.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7r1kC ![]() 1ispS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | ![]() Mass: 20483.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CIT / ![]() |
#3: Chemical | ChemComp-PO4 / ![]() |
#4: Chemical | ChemComp-PPI / ![]() |
#5: Water | ChemComp-HOH / ![]() |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.88 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES pH 6.5 18-22 % PEG 4000 0.1-0.5 M lithium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 0.87→35.07 Å / Num. obs: 103387 / % possible obs: 81.78 % / Redundancy: 6.1 % / Biso Wilson estimate: 7.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.028 / Net I/σ(I): 30.45 |
Reflection shell | Resolution: 0.87→0.9013 Å / Rmerge(I) obs: 0.4447 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 1919 / CC1/2: 0.786 / % possible all: 3.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1isp Resolution: 0.87→35.07 Å / SU ML: 0.0492 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 13.8355 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 1.3 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.87→35.07 Å
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Refine LS restraints |
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LS refinement shell |
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