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Yorodumi- PDB-6g6b: Crystal structure of a parallel six-helix coiled coil CC-Type2-LL-L17Q -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g6b | |||||||||
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Title | Crystal structure of a parallel six-helix coiled coil CC-Type2-LL-L17Q | |||||||||
Components | CC-Type2-LL-L17Q | |||||||||
Keywords | DE NOVO PROTEIN / de novo / coiled coil / alpha-helical bundle / synthetic construct | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | |||||||||
Authors | Rhys, G.G. / Brady, R.L. / Woolfson, D.N. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nat Commun / Year: 2018 Title: Maintaining and breaking symmetry in homomeric coiled-coil assemblies. Authors: Rhys, G.G. / Wood, C.W. / Lang, E.J.M. / Mulholland, 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 | 6g6b.cif.gz | 27.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g6b.ent.gz | 19.4 KB | Display | PDB format |
PDBx/mmJSON format | 6g6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g6b_validation.pdf.gz | 430.3 KB | Display | wwPDB validaton report |
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Full document | 6g6b_full_validation.pdf.gz | 430.3 KB | Display | |
Data in XML | 6g6b_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | 6g6b_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/6g6b ftp://data.pdbj.org/pub/pdb/validation_reports/g6/6g6b | HTTPS FTP |
-Related structure data
Related structure data | 6g65C 6g66C 6g67C 6g68C 6g69C 6g6aC 6g6cC 6g6dC 6g6eC 6g6fC 6g6gC 6g6hC 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: 3249.842 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: solid-phase peptide synthesis using the fmoc-based strategy 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: 4.92 Å3/Da / Density % sol: 74.99 % / Mosaicity: 0.25 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 50 mM SPG Buffer (Succinic acid, Sodium phosphate monobasic monohydrate and Glycine) and 12.5% w/v PEG 1500 |
-Data collection
Diffraction | Mean temperature: 80 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 19, 2016 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.3→74.1 Å / Num. obs: 9275 / % possible obs: 100 % / Redundancy: 65.4 % / Biso Wilson estimate: 53.46 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.01 / Rrim(I) all: 0.083 / Net I/σ(I): 38 / Num. measured all: 607009 / Scaling rejects: 6 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→74.098 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 27.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 131.37 Å2 / Biso mean: 60.5363 Å2 / Biso min: 36.11 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→74.098 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %
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