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Open data
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Basic information
Entry | Database: PDB / ID: 4yfo | ||||||
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Title | beta1_ex1 | ||||||
![]() | beta1_ex1 | ||||||
![]() | DE NOVO PROTEIN / synthetic protein / solenoid | ||||||
Function / homology | E3 ubiquitin-protein ligase SopA / Pectate Lyase C-like / 3 Solenoid / Mainly Beta![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Murray, J.W. / MacDonald, J.T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension. Authors: MacDonald, J.T. / Kabasakal, B.V. / Godding, D. / Kraatz, S. / Henderson, L. / Barber, J. / Freemont, P.S. / Murray, J.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.2 KB | Display | ![]() |
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PDB format | ![]() | 78.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.4 KB | Display | ![]() |
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Full document | ![]() | 426.4 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 12.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yc5C ![]() 4ycqC ![]() 4ydtC ![]() 4yeiC ![]() 5di5C ![]() 5dn0C ![]() 5dnsC ![]() 5dqaC ![]() 5draC ![]() 5dzbC 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26864.357 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.41 Å3/Da / Density % sol: 80.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 90 mM Bis Tris pH 5.5, 2.7 M sodium chloride / PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 3.39→107.83 Å / Num. all: 9607 / Num. obs: 9607 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Rmerge(I) obs: 0.129 / Net I/av σ(I): 14.3 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 3.39→3.48 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 4.3 / % possible all: 98.9 |
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Processing
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Refinement | Resolution: 3.39→39.68 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 34.523 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.538 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 113.294 Å2
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Refinement step | Cycle: LAST / Resolution: 3.39→39.68 Å
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Refine LS restraints |
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