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- PDB-5mfe: Designed armadillo repeat protein YIIIM5AII in complex with (RR)4... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mfe | ||||||
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Title | Designed armadillo repeat protein YIIIM5AII in complex with (RR)4 peptide | ||||||
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![]() | DE NOVO PROTEIN / Designed armadillo repeat protein / peptide binding | ||||||
Function / homology | Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hansen, S. / Ernst, P. / Reichen, C. / Ewald, C. / Mittl, P. / Plueckthun, A. | ||||||
![]() | ![]() Title: Curvature of designed armadillo repeat proteins allows modular peptide binding. Authors: Hansen, S. / Ernst, P. / Konig, S.L.B. / Reichen, C. / Ewald, C. / Nettels, D. / Mittl, P.R.E. / Schuler, B. / Pluckthun, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 432.7 KB | Display | ![]() |
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PDB format | ![]() | 357 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.4 KB | Display | ![]() |
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Full document | ![]() | 477.2 KB | Display | |
Data in XML | ![]() | 42.1 KB | Display | |
Data in CIF | ![]() | 61.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mfbC ![]() 5mffC ![]() 5mfgC ![]() 5mfhC ![]() 5mfiC ![]() 5mfjC ![]() 5mfkC ![]() 5mflC ![]() 5mfmC ![]() 5mfnC ![]() 5mfoC ![]() 5mfcS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30027.445 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #2: Protein/peptide | ( | Mass: 1275.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.65 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: PEG8000 5%, MPD 27.27%, NaCacodylate 0.1M pH7 200mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 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: 1.95→48.35 Å / Num. obs: 83955 / % possible obs: 99.9 % / Redundancy: 8.6 % / Biso Wilson estimate: 33.38 Å2 / Rmerge(I) obs: 0.241 / Net I/σ(I): 7.94 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 8.8 % / Rmerge(I) obs: 3.68 / Mean I/σ(I) obs: 0.6 / CC1/2: 0.155 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MFC Resolution: 1.95→48.35 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.156 / SU Rfree Blow DPI: 0.147 / SU Rfree Cruickshank DPI: 0.148
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Displacement parameters | Biso mean: 40.9 Å2
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Refine analyze | Luzzati coordinate error obs: 0.28 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.95→48.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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