[English] 日本語
Yorodumi- PDB-5tjd: Computer-based rational design of improved functionality for anti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tjd | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Computer-based rational design of improved functionality for antibody catalysts toward organophosphorus compounds | |||||||||
Components |
| |||||||||
Keywords | IMMUNE SYSTEM / Antibody / rational design | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Chatziefthimiou, S. / Stepanova, A. / Smirnov, I. / Gabibov, A. / Wilmanns, M. | |||||||||
Funding support | Germany, Russian Federation, 2items
| |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5tjd.cif.gz | 175.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5tjd.ent.gz | 138.2 KB | Display | PDB format |
PDBx/mmJSON format | 5tjd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/5tjd ftp://data.pdbj.org/pub/pdb/validation_reports/tj/5tjd | HTTPS FTP |
---|
-Related structure data
Related structure data | 6y1kC 6y1lC 6y1mC 6y1nC 6y49C 2xzcS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 24763.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella pastoris GS115 (fungus) |
---|---|
#2: Antibody | Mass: 26606.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella pastoris GS115 (fungus) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.86 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9673 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→49.35 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|