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Yorodumi- PDB-5led: Crystal structure of DARPin-DARPin rigid fusion, variant DDD_D12_... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5led | |||||||||
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Title | Crystal structure of DARPin-DARPin rigid fusion, variant DDD_D12_12_D12_12_D12 | |||||||||
Components | DDD_D12_12_D12_12_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: 2.6 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 | 5led.cif.gz | 257.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5led.ent.gz | 214.1 KB | Display | PDB format |
PDBx/mmJSON format | 5led.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5led_validation.pdf.gz | 413.3 KB | Display | wwPDB validaton report |
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Full document | 5led_full_validation.pdf.gz | 415.3 KB | Display | |
Data in XML | 5led_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 5led_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/5led ftp://data.pdbj.org/pub/pdb/validation_reports/le/5led | HTTPS FTP |
-Related structure data
Related structure data | 5le2C 5le3C 5le4C 5le6C 5le7C 5le8C 5le9C 5leaC 5lebC 5lecC 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: 52222.852 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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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 4000 20% w/v, Tris (HOAc) 0.1 M, Cadmium chloride 5 mM, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→47.806 Å / Num. obs: 14376 / % possible obs: 97.94 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.2551 / Net I/σ(I): 18.38 |
Reflection shell | Resolution: 2.6→2.693 Å / Rmerge(I) obs: 2.693 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SVX chain A Resolution: 2.6→47.806 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.01
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→47.806 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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