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- PDB-5u35: Crystal structure of a de novo designed protein with curved beta-sheet -
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Open data
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Basic information
Entry | Database: PDB / ID: 5u35 | ||||||
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Title | Crystal structure of a de novo designed protein with curved beta-sheet | ||||||
![]() | De novo NTF2 with large cavity | ||||||
![]() | DE NOVO PROTEIN / de novo NTF2 | ||||||
Function / homology | 2-METHOXYETHANOL / Chem-PG6![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oberdorfer, G. / Marcos, E. / Basanta, B. / Chidyausiku, T.M. / Sankaran, B. / Zwart, P.H. / Baker, D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.7 KB | Display | ![]() |
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PDB format | ![]() | 88.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 626.2 KB | Display | ![]() |
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Full document | ![]() | 628.6 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kpeC ![]() 5kphC ![]() 5l33C ![]() 5tphC ![]() 5tpjC ![]() 5trvC ![]() 5ts4C 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 14365.744 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET28b+ / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 150 molecules ![](data/chem/img/MXE.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PG6.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PG6.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MXE / #3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Chemical | ChemComp-PG6 / | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 35.29 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.3M Sodium fluoride, 0.3M Sodium bromide, 0.3M Sodium iodide, 0.1M Sodium HEPES, MOPS (acid) pH=7.5, 20% v/v PEG 500 MME, 10 % w/v PEG 20000 Temp details: Incubator |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999857 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→43.27 Å / Num. obs: 20381 / % possible obs: 99.9 % / Redundancy: 4.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.108 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.8 / CC1/2: 0.505 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 1.8→43.274 Å
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Refine LS restraints |
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LS refinement shell |
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