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- PDB-3zl4: Antibody structural organization: Role of kappa - lambda chain co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zl4 | ||||||
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Title | Antibody structural organization: Role of kappa - lambda chain constant domain switch in catalytic functionality | ||||||
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![]() | IMMUNE SYSTEM | ||||||
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 / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chatziefthimiou, S.D. / Ponomarenko, N.A. / Kurkova, I.N. / Smirnov, A.V. / Smirnov, I.V. / Lamzin, V.S. / Gabibov, A.G. / Wilmanns, M. | ||||||
![]() | ![]() Title: Role of Kappa>Lambda Light-Chain Constant-Domain Switch in the Structure and Functionality of A17 Reactibody Authors: Ponomarenko, N.A. / Chatziefthimiou, S.D. / Kurkova, I.N. / Mokrushina, Y.A. / Stepanova, A.V. / Smirnov, I.V. / Avakyan, E.M. / Bobik, T.V. / Mamedov, A. / Mitkevich, V.A. / Belogurov, A.J. ...Authors: Ponomarenko, N.A. / Chatziefthimiou, S.D. / Kurkova, I.N. / Mokrushina, Y.A. / Stepanova, A.V. / Smirnov, I.V. / Avakyan, E.M. / Bobik, T.V. / Mamedov, A. / Mitkevich, V.A. / Belogurov, A.J. / Fedorova, O.S. / Dubina, M. / Golovin, A. / Lamzin, V.S. / Friboulet, A. / Makarov, A.A. / Wilmanns, M. / Gabibov, A.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.3 KB | Display | ![]() |
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PDB format | ![]() | 79.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.1 KB | Display | ![]() |
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Full document | ![]() | 460 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xzaS S: Starting model for refinement |
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Similar 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: 27415.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 26115.768 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Chemical | ChemComp-MES / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1M MES PH 6.5, 0.25 M AMMONIUM SULFATE, 20% W/V PEG 5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 14, 2012 |
Radiation | Monochromator: SI(III) CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2234 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→25 Å / Num. obs: 39334 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XZA Resolution: 1.95→24.399 Å / SU ML: 0.23 / σ(F): 1.38 / Phase error: 26.92 / Stereochemistry target values: ML
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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: 25.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→24.399 Å
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Refine LS restraints |
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LS refinement shell |
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