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- PDB-8qag: X-ray crystal structure of a de novo designed single-chain parall... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qag | ||||||
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Title | X-ray crystal structure of a de novo designed single-chain parallel coiled-coil alpha-helical barrel with 6 inner helices, sc-CC-6-95 | ||||||
![]() | sc-CC-6-95 | ||||||
![]() | DE NOVO PROTEIN / coiled coil / alpha-helical barrel / de novo protein design | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Petrenas, R. / Albanese, K.I. / Woolfson, D.N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Rationally seeded computational protein design of ɑ-helical barrels. Authors: Albanese, K.I. / Petrenas, R. / Pirro, F. / Naudin, E.A. / Borucu, U. / Dawson, W.M. / Scott, D.A. / Leggett, G.J. / Weiner, O.D. / Oliver, T.A.A. / Woolfson, D.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 207.7 KB | Display | ![]() |
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PDB format | ![]() | 166.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.4 KB | Display | ![]() |
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Full document | ![]() | 454.9 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qaaC ![]() 8qabC ![]() 8qacC ![]() 8qadC ![]() 8qaeC ![]() 8qafC ![]() 8qahC ![]() 8qaiC ![]() 8qkdC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33562.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-PG4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.17 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 75% JCSG A6: 0.2 M lithium sulfate, 0.1 M phosphate-citrate pH 4.2, 20% PEG 1000. 25% Structure Screen 1 & 2 A11: 0.2 M calcium chloride dihydrate, 0.1 M sodium acetate, pH 4.6, 20% w/v 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→57.98 Å / Num. obs: 15396 / % possible obs: 99.83 % / Redundancy: 49.9 % / Biso Wilson estimate: 69.96 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1387 / Rpim(I) all: 0.02015 / Rrim(I) all: 0.1402 / Net I/σ(I): 15.29 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 50.6 % / Rmerge(I) obs: 0.6924 / Mean I/σ(I) obs: 1.87 / Num. unique obs: 1488 / CC1/2: 0.972 / CC star: 0.993 / Rpim(I) all: 0.0976 / Rrim(I) all: 0.6993 / % possible all: 99.07 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Waters and rotamer outliers were fixed with COOT(0.8.9.2).
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→57.98 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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