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Yorodumi- PDB-5l33: Crystal structure of a de novo designed protein with curved beta-sheet -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l33 | ||||||
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Title | Crystal structure of a de novo designed protein with curved beta-sheet | ||||||
Components | denovo NTF2 | ||||||
Keywords | DE NOVO PROTEIN / de novo NTF2 | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Oberdorfer, G. / Marcos, E. / Basanta, B. / Chidyausiku, T.M. / Sankaran, B. / Baker, D. | ||||||
Citation | Journal: Science / Year: 2017 Title: Principles for designing proteins with cavities formed by curved beta sheets. Authors: Marcos, E. / Basanta, B. / Chidyausiku, T.M. / Tang, Y. / Oberdorfer, G. / Liu, G. / Swapna, G.V. / Guan, R. / Silva, D.A. / Dou, J. / Pereira, J.H. / Xiao, R. / Sankaran, B. / Zwart, P.H. / ...Authors: Marcos, E. / Basanta, B. / Chidyausiku, T.M. / Tang, Y. / Oberdorfer, G. / Liu, G. / Swapna, G.V. / Guan, R. / Silva, D.A. / Dou, J. / Pereira, J.H. / Xiao, R. / Sankaran, B. / Zwart, P.H. / Montelione, G.T. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l33.cif.gz | 60.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l33.ent.gz | 43.7 KB | Display | PDB format |
PDBx/mmJSON format | 5l33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/5l33 ftp://data.pdbj.org/pub/pdb/validation_reports/l3/5l33 | HTTPS FTP |
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-Related structure data
Related structure data | 5kpeC 5kphC 5tphC 5tpjC 5trvC 5ts4C 5u35C 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: 12847.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: 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: 1.92 Å3/Da / Density % sol: 35.86 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium MOPS/HEPES, pH 7.5, 12.5% PEG 1000, 12.5% PEG 3350 and 12.5% 2-methyl-2,4-pentanediol and 0.2 M of amino acids (sodium glutamate, DL-alanine, glycine, DL-lysine HCl and DL-serine) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50.195 Å / Num. obs: 6503 / % possible obs: 92.3 % / Redundancy: 7.8 % / Net I/σ(I): 24.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50.195 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50.195 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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