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Yorodumi- PDB-7nfp: A heptameric barrel state of a de novo coiled-coil assembly: CC-T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nfp | |||||||||
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Title | A heptameric barrel state of a de novo coiled-coil assembly: CC-Type2-(LaId)4-I17K | |||||||||
Components | CC-Type2-(LaId)4-I17K | |||||||||
Keywords | DE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | |||||||||
Authors | Burton, A.J. / 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 | 7nfp.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nfp.ent.gz | 76 KB | Display | PDB format |
PDBx/mmJSON format | 7nfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nfp_validation.pdf.gz | 462.7 KB | Display | wwPDB validaton report |
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Full document | 7nfp_full_validation.pdf.gz | 463.9 KB | Display | |
Data in XML | 7nfp_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 7nfp_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/7nfp ftp://data.pdbj.org/pub/pdb/validation_reports/nf/7nfp | HTTPS FTP |
-Related structure data
Related structure data | 7nffC 7nfgC 7nfhC 7nfiC 7nfjC 7nfkC 7nflC 7nfmC 7nfnC 7nfoC 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
#1: Protein/peptide | Mass: 3406.903 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: 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: 2.61 Å3/Da / Density % sol: 52.81 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 0.1 M NaCl, 10% v/v 2-propanol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→44.67 Å / Num. obs: 46158 / % possible obs: 99.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 12.75 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.047 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.43→1.45 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2238 / CC1/2: 0.8 / Rpim(I) all: 0.437 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: model helices Resolution: 1.43→44.665 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→44.665 Å
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Refine LS restraints |
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LS refinement shell |
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