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Open data
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Basic information
Entry | Database: PDB / ID: 2yij | ||||||
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Title | Crystal Structure of phospholipase A1 | ||||||
![]() | PHOSPHOLIPASE A1-IIGAMMA | ||||||
![]() | HYDROLASE / PHOSPHOLIPASE | ||||||
Function / homology | ![]() diacylglycerol catabolic process / negative regulation of seed germination / monoacylglycerol catabolic process / phospholipase A1 activity / monoacylglycerol lipase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / lipid storage / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, I. | ||||||
![]() | ![]() Title: Crystal Structure of Phospholipase A1 Authors: Lee, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.5 KB | Display | ![]() |
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PDB format | ![]() | 138.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.6 KB | Display | ![]() |
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Full document | ![]() | 449.3 KB | Display | |
Data in XML | ![]() | 33.7 KB | Display | |
Data in CIF | ![]() | 48.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 48229.980 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: 2.77 Å3/Da / Density % sol: 55.57 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() | ||||||||||||
Detector | Type: ADSC CCD / Detector: CCD | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→30 Å / Num. obs: 114783 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 25.39 | ||||||||||||
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.45 / % possible all: 91.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2→19.92 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.887 / SU B: 0.003 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 3.999 / ESU R Free: 4.568 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||
Displacement parameters | Biso mean: 21.831 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.92 Å
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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