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- PDB-1jgv: STRUCTURAL BASIS FOR DISFAVORED ELIMINATION REACTION IN CATALYTIC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jgv | ||||||
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Title | STRUCTURAL BASIS FOR DISFAVORED ELIMINATION REACTION IN CATALYTIC ANTIBODY 1D4 | ||||||
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![]() | IMMUNE SYSTEM / IgG fold | ||||||
Function / homology | ![]() immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / immune response / extracellular space / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Larsen, N.A. / Heine, A. / Crane, L. / Cravatt, B.F. / Lerner, R.A. / Wilson, I.A. | ||||||
![]() | ![]() Title: Structural basis for a disfavored elimination reaction in catalytic antibody 1D4. Authors: Larsen, N.A. / Heine, A. / Crane, L. / Cravatt, B.F. / Lerner, R.A. / Wilson, I.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.3 KB | Display | ![]() |
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PDB format | ![]() | 77.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 407.7 KB | Display | ![]() |
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Full document | ![]() | 411.8 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 16.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 24206.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: purified from IgG derived from ascites fluid / Source: (natural) ![]() ![]() |
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#2: Antibody | Mass: 23650.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: purified from IgG derived from ascites fluid / Source: (natural) ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.67 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 4K, 10% isopropanol, 10% HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 23K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.5 / Method: unknown | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 13, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. all: 39285 / Num. obs: 39285 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.487 / % possible all: 98.8 |
Reflection | *PLUS Lowest resolution: 20 Å |
Reflection shell | *PLUS Lowest resolution: 1.88 Å / % possible obs: 98.8 % / Mean I/σ(I) obs: 2.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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