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Open data
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Basic information
Entry | Database: PDB / ID: 3u0v | ||||||
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Title | Crystal Structure Analysis of human LYPLAL1 | ||||||
![]() | Lysophospholipase-like protein 1 | ||||||
![]() | HYDROLASE / alpha / beta hydrolase fold | ||||||
Function / homology | ![]() palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / lysophospholipase activity / carboxylic ester hydrolase activity / hydrolase activity, acting on ester bonds / negative regulation of cGAS/STING signaling pathway / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Burger, M. / Zimmermann, T.J. / Kondoh, Y. / Stege, P. / Watanabe, N. / Osada, H. / Waldmann, H. / Vetter, I.R. | ||||||
![]() | ![]() Title: Crystal structure of the predicted phospholipase LYPLAL1 reveals unexpected functional plasticity despite close relationship to acyl protein thioesterases Authors: Burger, M. / Zimmermann, T.J. / Kondoh, Y. / Stege, P. / Watanabe, N. / Osada, H. / Waldmann, H. / Vetter, I.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.2 KB | Display | ![]() |
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PDB format | ![]() | 43.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.6 KB | Display | ![]() |
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Full document | ![]() | 441.6 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 17.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1fj2S 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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Unit cell |
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Components
#1: Protein | Mass: 26521.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q5VWZ2, Hydrolases; Acting on ester bonds; Thioester hydrolases |
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#2: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE IS BASED ON REF 1 AND 3 OF DATABASE UNIPROTKB/SWISSPROT Q5VWZ2 (LYPL1_HUMAN). I131M IS ...THE SEQUENCE IS BASED ON REF 1 AND 3 OF DATABASE UNIPROTKB/SWISSPROT Q5VWZ2 (LYPL1_HUMAN). I131M IS NATURAL VARIANT. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% w/v PEG 3350, 0.1M Bis-Tris pH 5.5, vapor diffusion, sitting drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.72→33.73 Å / Num. obs: 23960 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.419 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.54 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1fj2 Resolution: 1.72→33.73 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.1909 / WRfactor Rwork: 0.1582 / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.8823 / SU B: 1.941 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1099 / SU Rfree: 0.1088 / Cross valid method: THROUGHOUT / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.48 Å2 / Biso mean: 19.6591 Å2 / Biso min: 5.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→33.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.765 Å / Total num. of bins used: 20
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