[English] 日本語
Yorodumi- PDB-7nfh: A heptameric barrel state of a de novo coiled-coil assembly: CC-T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nfh | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | A heptameric barrel state of a de novo coiled-coil assembly: CC-Type2-(MaId)4. | |||||||||
Components | CC-Type2-(MaId)4 | |||||||||
Keywords | DE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | |||||||||
Authors | Rhys, G.G. / Dawson, W.M. / Brady, R.L. / Woolfson, D.N. | |||||||||
Funding support | European Union, United Kingdom, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7nfh.cif.gz | 104.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7nfh.ent.gz | 85.7 KB | Display | PDB format |
PDBx/mmJSON format | 7nfh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nfh_validation.pdf.gz | 468.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7nfh_full_validation.pdf.gz | 472.1 KB | Display | |
Data in XML | 7nfh_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 7nfh_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/7nfh ftp://data.pdbj.org/pub/pdb/validation_reports/nf/7nfh | HTTPS FTP |
-Related structure data
Related structure data | 7nffC 7nfgC 7nfiC 7nfjC 7nfkC 7nflC 7nfmC 7nfnC 7nfoC 7nfpC 8a09C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein/peptide | Mass: 3307.023 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-MES / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.79 Å3/Da / Density % sol: 67.52 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: After 1:1 dilution with the peptide solution, the resulting conditions were 250 mM ammonium sulfate and 50 mM 2-morpholinoethanesulfonic acid (MES). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 11, 2017 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.62→55.94 Å / Num. obs: 45086 / % possible obs: 99.7 % / Redundancy: 19.4 % / Biso Wilson estimate: 25.77 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.025 / Rrim(I) all: 0.109 / Net I/σ(I): 16.4 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 17.4 %
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: model helices Resolution: 1.62→55.94 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.7 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 108.16 Å2 / Biso mean: 33.413 Å2 / Biso min: 18.18 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.62→55.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.62→1.662 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|