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Yorodumi- PDB-6y1n: Crystal structure of the phosphonate-modified A.5 antibody FAB fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y1n | ||||||||||||
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Title | Crystal structure of the phosphonate-modified A.5 antibody FAB fragment | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / QM/MM computation / designed biocatalysts / bioscavengers / phosphoryl transfer / organophosphorus agents / stereospecificity | ||||||||||||
Function / homology | Chem-XOP Function and homology information | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||||||||
Authors | Chatziefthimiou, S. / Mokrushina, Y. / Smirnov, I. / Gabibov, A. / Wilmanns, M. | ||||||||||||
Funding support | Germany, Russian Federation, 3items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y1n.cif.gz | 99.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y1n.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 6y1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/6y1n ftp://data.pdbj.org/pub/pdb/validation_reports/y1/6y1n | HTTPS FTP |
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-Related structure data
Related structure data | 5tjdC 6y1kC 6y1lC 6y1mC 6y49C 2xzaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 27471.432 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella phaffii GS115 (fungus) |
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#2: Antibody | Mass: 26666.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella phaffii GS115 (fungus) |
#3: Chemical | ChemComp-XOP / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.68 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Ammonium citrate, pH 7.0, 1.7M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.106 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.106 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. obs: 20214 / % possible obs: 97.7 % / Redundancy: 12.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.081 / Rrim(I) all: 0.212 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.581 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1715 / CC1/2: 0.45 / Rpim(I) all: 0.683 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XZA Resolution: 2.2→24.258 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.52 / 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 max: 83.28 Å2 / Biso mean: 37.7548 Å2 / Biso min: 16.99 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→24.258 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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