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Yorodumi- PDB-6xxv: Crystal Structure of a computationally designed Immunogen S2_1.2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xxv | ||||||||||||
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Title | Crystal Structure of a computationally designed Immunogen S2_1.2 in complex with its elicited antibody C57 | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / epitope scaffold / de novo designed protein / immunogen | ||||||||||||
Function / homology | Ribosome-recycling factor / Topoisomerase I; Chain A, domain 4 / Orthogonal Bundle / Mainly Alpha Function and homology information | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.20116418766 Å | ||||||||||||
Authors | Yang, C. / Sesterhenn, F. / Correia, B.E. / Pojer, F. | ||||||||||||
Funding support | Switzerland, European Union, 3items
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Citation | Journal: Science / Year: 2020 Title: De novo protein design enables the precise induction of RSV-neutralizing antibodies. Authors: Sesterhenn, F. / Yang, C. / Bonet, J. / Cramer, J.T. / Wen, X. / Wang, Y. / Chiang, C.I. / Abriata, L.A. / Kucharska, I. / Castoro, G. / Vollers, S.S. / Galloux, M. / Dheilly, E. / Rosset, S. ...Authors: Sesterhenn, F. / Yang, C. / Bonet, J. / Cramer, J.T. / Wen, X. / Wang, Y. / Chiang, C.I. / Abriata, L.A. / Kucharska, I. / Castoro, G. / Vollers, S.S. / Galloux, M. / Dheilly, E. / Rosset, S. / Corthesy, P. / Georgeon, S. / Villard, M. / Richard, C.A. / Descamps, D. / Delgado, T. / Oricchio, E. / Rameix-Welti, M.A. / Mas, V. / Ervin, S. / Eleouet, J.F. / Riffault, S. / Bates, J.T. / Julien, J.P. / Li, Y. / Jardetzky, T. / Krey, T. / Correia, B.E. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xxv.cif.gz | 278.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xxv.ent.gz | 180.3 KB | Display | PDB format |
PDBx/mmJSON format | 6xxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/6xxv ftp://data.pdbj.org/pub/pdb/validation_reports/xx/6xxv | HTTPS FTP |
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-Related structure data
Related structure data | 6s3dC 6vtwC 6xwiC 4jlrS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 27005.182 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 25521.416 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Protein | Mass: 14478.467 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium tartrate dibasic, 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.97 Å / Num. obs: 67660 / % possible obs: 97.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 46.9217889225 Å2 / Rrim(I) all: 0.053 / Net I/σ(I): 22.59 |
Reflection shell | Resolution: 2.2→2.33 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 52096 / Rrim(I) all: 0.779 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JLR Resolution: 2.20116418766→48.97 Å / SU ML: 0.321425444791 / Cross valid method: NONE / σ(F): 1.35000269217 / Phase error: 27.8345679291
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.5994896265 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.20116418766→48.97 Å
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Refine LS restraints |
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LS refinement shell |
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