+Open data
-Basic information
Entry | Database: PDB / ID: 6ywd | ||||||||||||
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Title | De novo designed protein 4H_01 in complex with Mota antibody | ||||||||||||
Components |
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Keywords | DE NOVO PROTEIN / De novo designed protein | ||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||||||||
Authors | Yang, C. / Sesterhenn, F. / Pojer, F. / Correia, B.E. | ||||||||||||
Funding support | Switzerland, European Union, 3items
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Citation | Journal: Nat.Chem.Biol. / Year: 2021 Title: Bottom-up de novo design of functional proteins with complex structural features. Authors: Yang, C. / Sesterhenn, F. / Bonet, J. / van Aalen, E.A. / Scheller, L. / Abriata, L.A. / Cramer, J.T. / Wen, X. / Rosset, S. / Georgeon, S. / Jardetzky, T. / Krey, T. / Fussenegger, M. / ...Authors: Yang, C. / Sesterhenn, F. / Bonet, J. / van Aalen, E.A. / Scheller, L. / Abriata, L.A. / Cramer, J.T. / Wen, X. / Rosset, S. / Georgeon, S. / Jardetzky, T. / Krey, T. / Fussenegger, M. / Merkx, M. / 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 | 6ywd.cif.gz | 133.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ywd.ent.gz | 85.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ywd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ywd_validation.pdf.gz | 439.8 KB | Display | wwPDB validaton report |
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Full document | 6ywd_full_validation.pdf.gz | 444.7 KB | Display | |
Data in XML | 6ywd_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 6ywd_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/6ywd ftp://data.pdbj.org/pub/pdb/validation_reports/yw/6ywd | HTTPS FTP |
-Related structure data
Related structure data | 6ywcC 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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Unit cell |
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-Components
#1: Antibody | Mass: 25033.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23899.604 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#3: Protein | Mass: 10424.874 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.53 Å3/Da / Density % sol: 72.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M bicine pH 9.3, 22% v/v PEG Smear Broad |
-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: Feb 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→47.1 Å / Num. obs: 757244 / % possible obs: 99.8 % / Redundancy: 14.7 % / Biso Wilson estimate: 76.37 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.8→2.96 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 117130 / CC1/2: 0.56 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JLR Resolution: 3.2→47.04 Å / SU ML: 0.4546 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 25.983 / Stereochemistry target values: GeoStd + Monomer Library
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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: 75.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→47.04 Å
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Refine LS restraints |
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LS refinement shell |
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