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Yorodumi- PDB-7nfi: An octameric barrel state of a de novo coiled-coil assembly: CC-T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nfi | |||||||||
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Title | An octameric barrel state of a de novo coiled-coil assembly: CC-Type2-(LaId)4-L7Y. | |||||||||
Components | CC-Type2-(LaId)4-L7Y | |||||||||
Keywords | DE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | |||||||||
Authors | Rhys, G.G. / Dawson, W.M. / Brady, R.L. / Woolfson, D.N. | |||||||||
Funding support | European Union, United Kingdom, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Differential sensing with arrays of de novo designed peptide assemblies. Authors: Dawson, W.M. / Shelley, K.L. / Fletcher, J.M. / Scott, D.A. / Lombardi, L. / Rhys, G.G. / LaGambina, T.J. / Obst, U. / Burton, A.J. / Cross, J.A. / Davies, G. / Martin, F.J.O. / Wiseman, F.J. ...Authors: Dawson, W.M. / Shelley, K.L. / Fletcher, J.M. / Scott, D.A. / Lombardi, L. / Rhys, G.G. / LaGambina, T.J. / Obst, U. / Burton, A.J. / Cross, J.A. / Davies, G. / Martin, F.J.O. / Wiseman, F.J. / Brady, R.L. / Tew, D. / Wood, C.W. / 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 | 7nfi.cif.gz | 38.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nfi.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 7nfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nfi_validation.pdf.gz | 417 KB | Display | wwPDB validaton report |
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Full document | 7nfi_full_validation.pdf.gz | 417 KB | Display | |
Data in XML | 7nfi_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 7nfi_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/7nfi ftp://data.pdbj.org/pub/pdb/validation_reports/nf/7nfi | HTTPS FTP |
-Related structure data
Related structure data | 7nffC 7nfgC 7nfhC 7nfjC 7nfkC 7nflC 7nfmC 7nfnC 7nfoC 7nfpC 8a09C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 30 / Label seq-ID: 2 - 31
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-Components
#1: Protein/peptide | Mass: 3284.887 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: 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: 2.72 Å3/Da / Density % sol: 54.73 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: After 1:1 dilution with the peptide solution, the resulting conditions were 100 mM ammonium formate and 10% w/v PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 22, 2018 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.42→44.41 Å / Num. obs: 14194 / % possible obs: 100 % / Redundancy: 20.6 % / Biso Wilson estimate: 25.45 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.011 / Rrim(I) all: 0.049 / Net I/σ(I): 24.6 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: model helices Resolution: 1.42→44.41 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.321 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.063 / 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: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.95 Å2 / Biso mean: 30.615 Å2 / Biso min: 19.24 Å2
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Refinement step | Cycle: final / Resolution: 1.42→44.41 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 858 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.42→1.457 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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