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Open data
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Basic information
Entry | Database: PDB / ID: 7x0c | ||||||
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Title | Crystal structure of phospholipase A1, AtDSEL | ||||||
![]() | Phospholipase A1-IIgamma | ||||||
![]() | HYDROLASE / Phospholipase A1 | ||||||
Function / homology | ![]() diacylglycerol catabolic process / negative regulation of seed germination / monoacylglycerol catabolic process / phospholipase A1 activity / acylglycerol lipase activity / lipid storage / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Heo, Y. / Lee, I. / Moon, S. / Lee, W. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal Structures of the Plant Phospholipase A1 Proteins Reveal a Unique Dimerization Domain. Authors: Heo, Y. / Lee, I. / Moon, S. / Yun, J.H. / Kim, E.Y. / Park, S.Y. / Park, J.H. / Kim, W.T. / Lee, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 219.4 KB | Display | ![]() |
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PDB format | ![]() | 139.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.6 KB | Display | ![]() |
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Full document | ![]() | 440.6 KB | Display | |
Data in XML | ![]() | 32.8 KB | Display | |
Data in CIF | ![]() | 47.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7x0dC ![]() 2yijS 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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Unit cell |
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Components
#1: Protein | Mass: 47911.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O49523, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.02M calcium chloride, 0.1M sodium acetate, 30% MPD |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0082 Å / Relative weight: 1 |
Reflection | Resolution: 1.799→50 Å / Num. obs: 105892 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 22.0841058546 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 35.29 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 4586 |
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Processing
Software | Name: PHENIX / Version: 1.10.1_2155 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 2YIJ Resolution: 1.79909514333→33.2867143454 Å / SU ML: 0.167434903764 / Cross valid method: FREE R-VALUE / σ(F): 1.35431739796 / Phase error: 19.6841137382 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.9417230762 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79909514333→33.2867143454 Å
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Refine LS restraints |
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LS refinement shell |
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