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- PDB-8ia6: Crystal structure of scFv antibody against Phospholipase A2 of Ec... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ia6 | ||||||
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Title | Crystal structure of scFv antibody against Phospholipase A2 of Echis carinatus venom | ||||||
![]() | scFv antibody | ||||||
![]() | IMMUNE SYSTEM / scFv / snake venom / Phospholipase A2 / Echis carinatus | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, A. / Madni, Z.K. / Salunke, D.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of scFv antibody against Phospholipase A2 of Echis carinatus venom Authors: Kumar, A. / Madni, Z.K. / Salunke, D.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.7 KB | Display | ![]() |
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PDB format | ![]() | 76.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.1 KB | Display | ![]() |
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Full document | ![]() | 467.8 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 27.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 |
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Unit cell |
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Components
#1: Antibody | Mass: 26852.654 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.05 M Citric acid, 0.05 M Bis-Tris propane pH 5.0, 16% w/v Polyethylene glycol 3350 |
-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: Jul 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.988 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→33.35 Å / Num. obs: 15296 / % possible obs: 96.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 33.08 Å2 / CC1/2: 0.925 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1580 / CC1/2: 0.613 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 30.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→29.23 Å
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Refine LS restraints |
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LS refinement shell |
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