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- PDB-7nfn: A heptameric barrel state of a de novo coiled-coil assembly: CC-T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nfn | |||||||||
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Title | A heptameric barrel state of a de novo coiled-coil assembly: CC-Type2-(LaId)4-L21N-I24N. | |||||||||
![]() | CC-Type2-(LaId)4-L21N-I24N | |||||||||
![]() | DE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly | |||||||||
Function / homology | HEXANE-1,6-DIOL![]() | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rhys, G.G. / Dawson, W.M. / Brady, R.L. / Woolfson, D.N. | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 199.5 KB | Display | ![]() |
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PDB format | ![]() | 166 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 531.6 KB | Display | ![]() |
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Full document | ![]() | 536.4 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 32.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nffC ![]() 7nfgC ![]() 7nfhC ![]() 7nfiC ![]() 7nfjC ![]() 7nfkC ![]() 7nflC ![]() 7nfmC ![]() 7nfoC ![]() 7nfpC ![]() 8a09C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 3350.919 Da / Num. of mol.: 14 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-HEZ / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.52 % |
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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 100 mM magnesium chloride hexahydrate, 50 mM 2-amino-2-(hydroxymethyl)propane-1,3-diol (TRIS) and 1.7 M 1,6-hexanediol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 12, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.45→44.16 Å / Num. obs: 79988 / % possible obs: 95.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.032 / Rrim(I) all: 0.06 / Net I/σ(I): 10.6 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: model helices Resolution: 1.45→44.16 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.57 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.061 / 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: 102.29 Å2 / Biso mean: 21.324 Å2 / Biso min: 9.72 Å2
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Refinement step | Cycle: final / Resolution: 1.45→44.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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