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- PDB-8qae: X-ray crystal structure of a de novo designed single-chain antipa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qae | ||||||
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Title | X-ray crystal structure of a de novo designed single-chain antiparallel 6-helix alpha-helical barrel, sc-apCC-6-SLLA | ||||||
![]() | sc-apCC-6-SLLA | ||||||
![]() | DE NOVO PROTEIN / coiled coil / alpha-helical barrel / de novo protein design | ||||||
Function / homology | : ![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Albanese, K.I. / Petrenas, R. / 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 | ![]() | 208.3 KB | Display | ![]() |
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PDB format | ![]() | 137.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 576.2 KB | Display | ![]() |
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Full document | ![]() | 578.2 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qaaC ![]() 8qabC ![]() 8qacC ![]() 8qadC ![]() 8qafC ![]() 8qagC ![]() 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 on special symmetry positions |
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Components
#1: Protein | Mass: 26109.238 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #2: Chemical | ChemComp-P5R / | Mass: 766.909 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H70O18 #3: Chemical | ChemComp-1PE / | #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: 2.33 Å3/Da / Density % sol: 47.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M CaCl2, 0.1 M MES pH 6.0, 20% w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 6, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→21.4 Å / Num. obs: 25168 / % possible obs: 99.84 % / Redundancy: 6.7 % / Biso Wilson estimate: 35.49 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.08096 / Rpim(I) all: 0.03443 / Rrim(I) all: 0.08813 / Net I/σ(I): 14.57 |
Reflection shell | Resolution: 1.9→1.98 Å / Redundancy: 6 % / Rmerge(I) obs: 0.4644 / Mean I/σ(I) obs: 1.66 / Num. unique obs: 2501 / CC1/2: 0.903 / CC star: 0.974 / Rpim(I) all: 0.2069 / Rrim(I) all: 0.5099 / % possible all: 99.92 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→21.4 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 | Refine-ID: X-RAY DIFFRACTION
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