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Yorodumi- PDB-5j0h: De novo design of protein homo-oligomers with modular hydrogen bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j0h | |||||||||
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Title | De novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity | |||||||||
Components | Design construct 2L6HC3_13 | |||||||||
Keywords | DE NOVO PROTEIN / rosetta / de novo design | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | |||||||||
Authors | Sankaran, B. / Zwart, P.H. / Pereira, J.H. / Baker, D. / Boyken, S. / Chen, Z. / Groves, B. / Langan, R.A. / Oberdorfer, G. / Ford, A. ...Sankaran, B. / Zwart, P.H. / Pereira, J.H. / Baker, D. / Boyken, S. / Chen, Z. / Groves, B. / Langan, R.A. / Oberdorfer, G. / Ford, A. / Gilmore, J. / Xu, C. / DiMaio, F. / Seelig, G. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Science / Year: 2016 Title: De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity. Authors: Boyken, S.E. / Chen, Z. / Groves, B. / Langan, R.A. / Oberdorfer, G. / Ford, A. / Gilmore, J.M. / Xu, C. / DiMaio, F. / Pereira, J.H. / Sankaran, B. / Seelig, G. / Zwart, P.H. / Baker, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j0h.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j0h.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 5j0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/5j0h ftp://data.pdbj.org/pub/pdb/validation_reports/j0/5j0h | HTTPS FTP |
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-Related structure data
Related structure data | 5izsC 5j0iC 5j0jC 5j0kC 5j0lC 5j10C 5j2lC 5j73C 5jqzC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | Trimer according to SEC-MALS and SAXS data |
-Components
#1: Protein | Mass: 9143.416 Da / Num. of mol.: 2 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: 2.07 Å3/Da / Density % sol: 40.71 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.06 M Citric acid, 0.04 M BIS-TRIS propane pH 4.1, 16% 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: Oct 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→45.45 Å / Num. obs: 19278 / % possible obs: 99.96 % / Redundancy: 6.1 % / Net I/σ(I): 10.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→45.45 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 19.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→45.45 Å
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Refine LS restraints |
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LS refinement shell |
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