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Yorodumi- PDB-6q5s: Crystal structure of a de novo designed antiparallel four-helix c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q5s | ||||||||||||||||||
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Title | Crystal structure of a de novo designed antiparallel four-helix coiled coil apCC-Tet | ||||||||||||||||||
Components | apCC-Tet | ||||||||||||||||||
Keywords | DE NOVO PROTEIN / coiled coil / synthetic / antiparallel / tetramer | ||||||||||||||||||
Biological species | synthetic construct (others) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||||||||||||||
Authors | Beesley, J.L. / Guto, G.R. / Wood, C.W. / Brady, R.L. / Woolfson, D.N. | ||||||||||||||||||
Funding support | United Kingdom, Belgium, 5items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2019 Title: Navigating the Structural Landscape of De Novo alpha-Helical Bundles. Authors: Rhys, G.G. / Wood, C.W. / Beesley, J.L. / Zaccai, N.R. / Burton, A.J. / Brady, R.L. / Thomson, A.R. / Woolfson, D.N. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q5s.cif.gz | 55 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q5s.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 6q5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/6q5s ftp://data.pdbj.org/pub/pdb/validation_reports/q5/6q5s | HTTPS FTP |
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-Related structure data
Related structure data | 6q5hC 6q5iC 6q5jC 6q5kC 6q5lC 6q5mC 6q5nC 6q5oC 6q5pC 6q5qC 6q5rC 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/peptide | Mass: 3234.871 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.15 M sodium chloride, 50 mM sodium HEPES |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2018 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97628 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.89→48.96 Å / Num. obs: 13052 / % possible obs: 100 % / Redundancy: 25.2 % / Biso Wilson estimate: 24.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.04 / Rrim(I) all: 0.149 / Net I/σ(I): 15.1 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→48.957 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.62 / Stereochemistry target values: ML
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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: 1.89→48.957 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -18.8805 Å / Origin y: 2.7394 Å / Origin z: 14.7277 Å
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Refinement TLS group | Selection details: all |