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Yorodumi- PDB-7bo8: A hexameric de novo coiled-coil assembly: CC-Type2-(VaYd)4-Y3F-W1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bo8 | |||||||||
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Title | A hexameric de novo coiled-coil assembly: CC-Type2-(VaYd)4-Y3F-W19(BrPhe)-Y24F. | |||||||||
Components | CC-Type2-(VaYd)4-Y3F-W19(BrPhe)-Y24F | |||||||||
Keywords | DE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly / tyrosine-tyrosine interactions | |||||||||
Function / homology | OXAMIC ACID Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.84 Å | |||||||||
Authors | Rhys, G.G. / Brady, R.L. / Woolfson, D.N. | |||||||||
Funding support | European Union, United Kingdom, 2items
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Citation | Journal: Biomacromolecules / Year: 2021 Title: How Coiled-Coil Assemblies Accommodate Multiple Aromatic Residues. Authors: Rhys, G.G. / Dawson, W.M. / Beesley, J.L. / Martin, F.J.O. / 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 | 7bo8.cif.gz | 43.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bo8.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 7bo8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bo8_validation.pdf.gz | 487.3 KB | Display | wwPDB validaton report |
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Full document | 7bo8_full_validation.pdf.gz | 487.5 KB | Display | |
Data in XML | 7bo8_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 7bo8_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/7bo8 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/7bo8 | HTTPS FTP |
-Related 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: 3386.687 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-OXM / | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.28 Å3/Da / Density % sol: 46.13 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: After 1:1 dilution with the peptide solution the resulting conditions were 0.05 M Sodium formate, 0.05 M Ammonium acetate, 0.05 M Sodium citrate tribasic dihydrate, 0.05 M Potassium sodium ...Details: After 1:1 dilution with the peptide solution the resulting conditions were 0.05 M Sodium formate, 0.05 M Ammonium acetate, 0.05 M Sodium citrate tribasic dihydrate, 0.05 M Potassium sodium tartrate tetrahydrate, 0.05 M Sodium oxamate, 0.05 M Tris, 0.05 M BICINE, 6% v/v Ethylene glycol and 3% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91983 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 5, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91983 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.84→38.57 Å / Num. obs: 16884 / % possible obs: 99.9 % / Redundancy: 32.1 % / Biso Wilson estimate: 45.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.03 / Rrim(I) all: 0.176 / Net I/σ(I): 11.3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.84→38.57 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.208 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.15 Å2 / Biso mean: 47.797 Å2 / Biso min: 32.22 Å2
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Refinement step | Cycle: final / Resolution: 1.84→38.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.888 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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