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Yorodumi- PDB-6q5q: Crystal structure of a CC-Hex mutant that forms an antiparallel f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q5q | ||||||||||||||||||
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Title | Crystal structure of a CC-Hex mutant that forms an antiparallel four-helix coiled coil CC-Hex-KgEb | ||||||||||||||||||
Components | CC-Hex-KgEb | ||||||||||||||||||
Keywords | DE NOVO PROTEIN / coiled coil / tetramer / synthetic / antiparallel | ||||||||||||||||||
Function / homology | L(+)-TARTARIC ACID Function and homology information | ||||||||||||||||||
Biological species | synthetic construct (others) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.08 Å | ||||||||||||||||||
Authors | Zaccai, N.R. / Rhys, G.G. / Wood, C.W. / Beesley, J.L. / 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 | 6q5q.cif.gz | 23.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q5q.ent.gz | 17.3 KB | Display | PDB format |
PDBx/mmJSON format | 6q5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q5q_validation.pdf.gz | 433.8 KB | Display | wwPDB validaton report |
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Full document | 6q5q_full_validation.pdf.gz | 433.8 KB | Display | |
Data in XML | 6q5q_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 6q5q_validation.cif.gz | 5.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/6q5q ftp://data.pdbj.org/pub/pdb/validation_reports/q5/6q5q | HTTPS FTP |
-Related structure data
Related structure data | 6q5hC 6q5iC 6q5jC 6q5kC 6q5lC 6q5mC 6q5nC 6q5oC 6q5pC 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: 3363.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Antiparallel four-helix coiled coil / Source: (synth.) synthetic construct (others) |
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#2: Chemical | ChemComp-TLA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.74 Å3/Da / Density % sol: 29.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2M potassium/sodium tartrate tetrahydrate 20% w/v PEG 3350. |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→20.47 Å / Num. obs: 10348 / % possible obs: 99.7 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.021 / Rrim(I) all: 0.077 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.08→1.14 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 56.2 / Num. unique obs: 1461 / CC1/2: 0.943 / Rrim(I) all: 0.737 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.08→16.5 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.1 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.028 / 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: 14.091 Å2
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Refinement step | Cycle: 1 / Resolution: 1.08→16.5 Å
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Refine LS restraints |
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