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Yorodumi- PDB-5oos: Designed Ankyrin Repeat Protein (DARPin) YTRL-2 selected by direc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oos | ||||||
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Title | Designed Ankyrin Repeat Protein (DARPin) YTRL-2 selected by directed evolution against Lysozyme | ||||||
Components | DARPin YTRL-2 | ||||||
Keywords | DE NOVO PROTEIN / DARPin / directed evolution / designed protein | ||||||
Function / homology | Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||
Authors | Hogan, B.J. / Fischer, G. / Houlihan, G. / Edmond, S. / Huovinen, T.T.K. / Hollfelder, F. / Hyvonen, M. | ||||||
Citation | Journal: To be published Title: Designed Ankyrin Repeat Protein (DARPin) YTRL-2 selected by directed evolution against Lysozyme Authors: Fischer, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oos.cif.gz | 45.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oos.ent.gz | 31.7 KB | Display | PDB format |
PDBx/mmJSON format | 5oos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oos_validation.pdf.gz | 700.7 KB | Display | wwPDB validaton report |
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Full document | 5oos_full_validation.pdf.gz | 701.5 KB | Display | |
Data in XML | 5oos_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 5oos_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/5oos ftp://data.pdbj.org/pub/pdb/validation_reports/oo/5oos | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18161.377 Da / Num. of mol.: 1 / Fragment: DARPin / Mutation: YTRL-2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pQE30 / Production host: Escherichia coli M15 (bacteria) |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-2PE / |
#4: 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: 4.04 Å3/Da / Density % sol: 69.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 / Details: 30% PEG3000, 0.1M Tris pH=7, 0.2M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 1, 2017 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.259→65.393 Å / Num. obs: 14609 / % possible obs: 100 % / Redundancy: 52.3 % / Biso Wilson estimate: 66.59 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.014 / Rrim(I) all: 0.104 / Net I/σ(I): 33.4 / Num. measured all: 764056 | ||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→65.39 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU R Cruickshank DPI: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.176 / SU Rfree Blow DPI: 0.158 / SU Rfree Cruickshank DPI: 0.153
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Displacement parameters | Biso max: 144.34 Å2 / Biso mean: 66.45 Å2 / Biso min: 36.71 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.26→65.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.26→2.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
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