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Yorodumi- PDB-7bat: A hexameric barrel state of a de novo coiled-coil assembly: CC-Ty... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bat | ||||||||||||
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Title | A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(GgIaId)4 | ||||||||||||
Components | CC-Type2-(GgIaId)4 | ||||||||||||
Keywords | DE NOVO PROTEIN / alpha / helical / barrel / hexamer | ||||||||||||
Function / homology | N-PROPANOL Function and homology information | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.77 Å | ||||||||||||
Authors | Martin, F.J.O. / Dawson, W.M. / Shelley, K. / Brady, R.L. / Woolfson, D.N. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Chem Sci / Year: 2021 Title: Coiled coils 9-to-5: rational de novo design of alpha-helical barrels with tunable oligomeric states. Authors: Dawson, W.M. / Martin, F.J.O. / Rhys, G.G. / Shelley, K.L. / Brady, R.L. / 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 | 7bat.cif.gz | 41 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bat.ent.gz | 31.1 KB | Display | PDB format |
PDBx/mmJSON format | 7bat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bat_validation.pdf.gz | 443.6 KB | Display | wwPDB validaton report |
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Full document | 7bat_full_validation.pdf.gz | 444.2 KB | Display | |
Data in XML | 7bat_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 7bat_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/7bat ftp://data.pdbj.org/pub/pdb/validation_reports/ba/7bat | HTTPS FTP |
-Related structure data
Related structure data | 7a1tC 7basC 7bauC 7bavC 7bawC 7bimC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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:
NCS ensembles :
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-Components
#1: Protein/peptide | Mass: 3178.767 Da / Num. of mol.: 3 / 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: 2.82 Å3/Da / Density % sol: 56.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.5 mM peptide, 50 mM MES, 5 % w/v PEG 5000 MME, 6 % v/v 1-propanol. Temp details: 20 degC 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: Feb 16, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.77→40.48 Å / Num. obs: 10914 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.012 / Rrim(I) all: 0.041 / Net I/σ(I): 21.6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.77→40.48 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.617 / SU ML: 0.094 / SU R Cruickshank DPI: 0.1321 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.116 / 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: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.32 Å2 / Biso mean: 46.427 Å2 / Biso min: 31.74 Å2
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Refinement step | Cycle: final / Resolution: 1.77→40.48 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.77→1.816 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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