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- PDB-5tjd: Computer-based rational design of improved functionality for anti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5tjd | |||||||||
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Title | Computer-based rational design of improved functionality for antibody catalysts toward organophosphorus compounds | |||||||||
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![]() | IMMUNE SYSTEM / Antibody / rational design | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Chatziefthimiou, S. / Stepanova, A. / Smirnov, I. / Gabibov, A. / Wilmanns, M. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Multiscale computation delivers organophosphorus reactivity and stereoselectivity to immunoglobulin scavengers. Authors: Mokrushina, Y.A. / Golovin, A.V. / Smirnov, I.V. / Chatziefthimiou, S.D. / Stepanova, A.V. / Bobik, T.V. / Zalevsky, A.O. / Zlobin, A.S. / Konovalov, K.A. / Terekhov, S.S. / Stepanov, A.V. / ...Authors: Mokrushina, Y.A. / Golovin, A.V. / Smirnov, I.V. / Chatziefthimiou, S.D. / Stepanova, A.V. / Bobik, T.V. / Zalevsky, A.O. / Zlobin, A.S. / Konovalov, K.A. / Terekhov, S.S. / Stepanov, A.V. / Pipiya, S.O. / Shamborant, O.G. / Round, E. / Belogurov Jr., A.A. / Bourenkov, G. / Makarov, A.A. / Wilmanns, M. / Xie, J. / Blackburn, G.M. / Gabibov, A.G. / Lerner, R.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 | ![]() | 175.6 KB | Display | ![]() |
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PDB format | ![]() | 138.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.5 KB | Display | ![]() |
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Full document | ![]() | 426.1 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y1kC ![]() 6y1lC ![]() 6y1mC ![]() 6y1nC ![]() 6y49C ![]() 2xzcS S: Starting model for refinement C: citing same article ( |
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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: 24763.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 26606.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.86 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M ADA pH 7.5 0.17 M MgCl2 20% (w/v) PEG-6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9673 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→49.35 Å / Num. obs: 24892 / % possible obs: 98.81 % / Redundancy: 4.7 % / Biso Wilson estimate: 39.43 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08762 / Net I/σ(I): 10.43 |
Reflection shell | Resolution: 2.1→2.175 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 1.33 / CC1/2: 0.62 / % possible all: 97.07 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2xzc Resolution: 2.1→49.35 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 30.94
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→49.35 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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