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Yorodumi- PDB-5k7v: Computational Design of Self-Assembling Cyclic Protein Homooligomers -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k7v | ||||||
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Title | Computational Design of Self-Assembling Cyclic Protein Homooligomers | ||||||
Components | Designed protein HR00C3Design | ||||||
Keywords | DE NOVO PROTEIN / rosetta / de novo design | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.165 Å | ||||||
Authors | Sankaran, B. / Zwart, P.H. / Fallas, J.A. / Pereira, J.H. / Ueda, G. / Baker, D. | ||||||
Citation | Journal: Nat Chem / Year: 2017 Title: Computational design of self-assembling cyclic protein homo-oligomers. Authors: Fallas, J.A. / Ueda, G. / Sheffler, W. / Nguyen, V. / McNamara, D.E. / Sankaran, B. / Pereira, J.H. / Parmeggiani, F. / Brunette, T.J. / Cascio, D. / Yeates, T.R. / Zwart, P. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k7v.cif.gz | 303.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k7v.ent.gz | 254.8 KB | Display | PDB format |
PDBx/mmJSON format | 5k7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/5k7v ftp://data.pdbj.org/pub/pdb/validation_reports/k7/5k7v | HTTPS FTP |
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-Related structure data
Related structure data | 4gmrC 4gpmC 4hb5C 4hxtC 5hryC 5hrzC 5hs0C 5kbaC 5kwdC 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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Details | Trimer according to SAXS |
-Components
#1: Protein | Mass: 31442.357 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #2: Water | ChemComp-HOH / | |
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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: 3.67 Å3/Da / Density % sol: 66.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.3 M Sodium Citrate, 0.1 M Hepes pH 7.5 and 15 % PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.16→46 Å / Num. obs: 23543 / % possible obs: 98 % / Redundancy: 9.8 % / Net I/σ(I): 13 |
-Processing
Software |
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Refinement | Resolution: 3.165→46 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.165→46 Å
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Refine LS restraints |
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LS refinement shell |
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