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Yorodumi- PDB-8a09: A hexameric barrel state of a de novo coiled-coil assembly: CC-Ty... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a09 | ||||||||||||||||||
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Title | A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4 | ||||||||||||||||||
Components | A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4 | ||||||||||||||||||
Keywords | DE NOVO PROTEIN | ||||||||||||||||||
Biological species | synthetic construct (others) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.35 Å | ||||||||||||||||||
Authors | Martin, F.J.O. / Rhys, G.G. / Dawson, W.M. / Woolfson, D.N. | ||||||||||||||||||
Funding support | European Union, United Kingdom, 5items
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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 | 8a09.cif.gz | 37.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a09.ent.gz | 26.2 KB | Display | PDB format |
PDBx/mmJSON format | 8a09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/8a09 ftp://data.pdbj.org/pub/pdb/validation_reports/a0/8a09 | HTTPS FTP |
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-Related structure data
Related structure data | 7nffC 7nfgC 7nfhC 7nfiC 7nfjC 7nfkC 7nflC 7nfmC 7nfnC 7nfoC 7nfpC C: citing same article (ref.) |
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-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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-Components
#1: Protein/peptide | Mass: 3463.075 Da / Num. of mol.: 2 / 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: 1.86 Å3/Da / Density % sol: 33.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5 Details: 1.5 mM peptide, 50 mM Sodium acetate, 1% w/v PEG 4000 at pH 5.0 Temp details: Incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→32.85 Å / Num. obs: 10984 / % possible obs: 99.79 % / Redundancy: 5.2 % / Biso Wilson estimate: 20.91 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.1462 / Rpim(I) all: 0.06936 / Rrim(I) all: 0.162 / Net I/σ(I): 13.01 |
Reflection shell | Resolution: 1.35→1.398 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.009 / Mean I/σ(I) obs: 0.77 / Num. unique obs: 1089 / CC1/2: 0.529 / Rpim(I) all: 0.5337 / Rrim(I) all: 1.145 / % possible all: 99.91 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.35→32.85 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.992 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0695 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.49 Å2 / Biso mean: 25.972 Å2 / Biso min: 15.31 Å2
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Refinement step | Cycle: final / Resolution: 1.35→32.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.383 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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