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Yorodumi- PDB-5leb: Crystal structure of DARPin-DARPin rigid fusion, variant DDD_D12_... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5leb | |||||||||
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Title | Crystal structure of DARPin-DARPin rigid fusion, variant DDD_D12_06_D12_06_D12 | |||||||||
Components | DDD_D12_06_D12_06_D12 | |||||||||
Keywords | DE NOVO PROTEIN / designed ankyrin repeat proteins / protein design / protein engineering / rigid domain fusions | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Batyuk, A. / Wu, Y. / Mittl, P.R. / Plueckthun, A. | |||||||||
Funding support | Switzerland, 2items
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Citation | Journal: Sci Rep / Year: 2017 Title: Rigidly connected multispecific artificial binders with adjustable geometries. Authors: Wu, Y. / Batyuk, A. / Honegger, A. / Brandl, F. / Mittl, P.R.E. / Pluckthun, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5leb.cif.gz | 256.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5leb.ent.gz | 215.3 KB | Display | PDB format |
PDBx/mmJSON format | 5leb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5leb_validation.pdf.gz | 412.4 KB | Display | wwPDB validaton report |
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Full document | 5leb_full_validation.pdf.gz | 413 KB | Display | |
Data in XML | 5leb_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 5leb_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/5leb ftp://data.pdbj.org/pub/pdb/validation_reports/le/5leb | HTTPS FTP |
-Related structure data
Related structure data | 5le2C 5le3C 5le4C 5le6C 5le7C 5le8C 5le9C 5leaC 5lecC 5ledC 5leeC 5lelC 5lemC 5lw2C 1svxS 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
#1: Protein | Mass: 50522.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): XL1-Blue |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 8000 10.0% w/v, PEG 1000 10.0% w/v, Sodium acetate 0.3 M, Sodium cacodylate 0.1 M, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→35.343 Å / Num. obs: 24249 / % possible obs: 99.79 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 18.17 |
Reflection shell | Resolution: 2.3→2.382 Å / Rmerge(I) obs: 1.931 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SVX chain A Resolution: 2.3→35.343 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→35.343 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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