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Yorodumi- PDB-6q5m: Crystal structure of a CC-Hex mutant that forms an antiparallel f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q5m | ||||||||||||||||||||||||||||||||||||||
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Title | Crystal structure of a CC-Hex mutant that forms an antiparallel four-helix coiled coil CC-Hex*-L24Dab | ||||||||||||||||||||||||||||||||||||||
Components | CC-Hex*Keywords | DE NOVO PROTEIN / coiled coil / tetramer / synthetic / antiparallel / CC-Hex | Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | Authors | Wood, C.W. / Beesley, J.L. / Rhys, G.G. / Brady, R.L. / Woolfson, D.N. | Funding support | United Kingdom, Belgium, 5items |
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 | 6q5m.cif.gz | 21.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q5m.ent.gz | 15.4 KB | Display | PDB format |
PDBx/mmJSON format | 6q5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q5m_validation.pdf.gz | 432.6 KB | Display | wwPDB validaton report |
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Full document | 6q5m_full_validation.pdf.gz | 432.7 KB | Display | |
Data in XML | 6q5m_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 6q5m_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/6q5m ftp://data.pdbj.org/pub/pdb/validation_reports/q5/6q5m | HTTPS FTP |
-Related structure data
Related structure data | 6q5hC 6q5iC 6q5jC 6q5kC 6q5lC 6q5nC 6q5oC 6q5pC 6q5qC 6q5rC 6q5sC 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 on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 3221.832 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-NA / | #3: 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: 2.02 Å3/Da / Density % sol: 39.11 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.8 M Na/K hydrogen phosphate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9783 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9783 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.5→35.72 Å / Num. obs: 8775 / % possible obs: 98.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 16.469 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.036 / Rrim(I) all: 0.061 / Net I/σ(I): 12 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→35.72 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.944 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.081 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.245 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→35.72 Å
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Refine LS restraints |
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