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Open data
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Basic information
Entry | Database: PDB / ID: 4aup | ||||||
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Title | Tuber borchii Phospholipase A2 | ||||||
![]() | PHOSPHOLIPASE A2 GROUP XIII | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cavazzini, D. / Meschi, F. / Corsini, R. / Bolchi, A. / Rossi, G.-L. / Einsle, O. / Ottonello, S. | ||||||
![]() | ![]() Title: Autoproteolytic Activation of a Symbiosis-Regulated Truffle Phospholipase A2 Authors: Cavazzini, D. / Meschi, F. / Corsini, R. / Bolchi, A. / Rossi, G.-L. / Einsle, O. / Ottonello, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.3 KB | Display | ![]() |
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PDB format | ![]() | 91.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.5 KB | Display | ![]() |
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Full document | ![]() | 456.9 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 20 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14213.929 Da / Num. of mol.: 2 / Fragment: ACTIVE FORM, RESIDUES 89-211 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-SCN / | #4: Water | ChemComp-HOH / | Sequence details | STRUCTURE REPRESENTS AN AUTOPROTEOLYTICALLY PROCESSED FRAGMENT OF THE ENTIRE SEQUENCE. THE FIRST 91 ...STRUCTURE REPRESENTS | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.3 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 2.0 M AMMONIUM SULPHATE, 0.1 M HEPES, PH 7.5 2% PEG 200 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 22164 / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.85 / % possible all: 92.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.9→19.41 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / SU B: 8.929 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.173 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.408 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.41 Å
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Refine LS restraints |
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