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Yorodumi- PDB-5le9: Crystal structure of DARPin-DARPin rigid fusion, variant DD_Off7_... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5le9 | ||||||
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Title | Crystal structure of DARPin-DARPin rigid fusion, variant DD_Off7_09_3G124 | ||||||
Components | DD_Off7_09_3G124 | ||||||
Keywords | DE NOVO PROTEIN / designed ankyrin repeat proteins / protein design / protein engineering / rigid domain fusions | ||||||
Function / homology | ACETATE ION Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Batyuk, A. / Wu, Y. / Mittl, P.R. / Plueckthun, A. | ||||||
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 | 5le9.cif.gz | 186.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5le9.ent.gz | 152.4 KB | Display | PDB format |
PDBx/mmJSON format | 5le9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5le9_validation.pdf.gz | 438.2 KB | Display | wwPDB validaton report |
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Full document | 5le9_full_validation.pdf.gz | 439.5 KB | Display | |
Data in XML | 5le9_validation.xml.gz | 14 KB | Display | |
Data in CIF | 5le9_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/5le9 ftp://data.pdbj.org/pub/pdb/validation_reports/le/5le9 | HTTPS FTP |
-Related structure data
Related structure data | 5le2C 5le3C 5le4C 5le6C 5le7C 5le8C 5leaC 5lebC 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: 34980.469 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: Chemical | ChemComp-ACT / #3: 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: 2.37 Å3/Da / Density % sol: 48.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: MPD 30% v/v, Sodium chloride 0.2 M, Sodium acetate trihydrate 0.1 M, pH 4.6 |
-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: Dec 3, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→39.859 Å / Num. obs: 29498 / % possible obs: 99.44 % / Redundancy: 24.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1782 / Net I/σ(I): 13.26 |
Reflection shell | Resolution: 1.85→1.916 Å / Rmerge(I) obs: 18.36 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SVX chain A Resolution: 1.85→39.859 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→39.859 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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