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Yorodumi- PDB-5w0j: Antiparallel coiled coil hexamer formed by de novo peptides (ACC-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w0j | |||||||||
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Title | Antiparallel coiled coil hexamer formed by de novo peptides (ACC-Hex2). | |||||||||
Components | peptide 1 | |||||||||
Keywords | DE NOVO PROTEIN / antiparallel / hexamer / de novo / phe-ile zipper | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.201 Å | |||||||||
Authors | Spencer, R.K. / Hochbaum, A.I. | |||||||||
Citation | Journal: Biochemistry / Year: 2017 Title: The Phe-Ile Zipper: A Specific Interaction Motif Drives Antiparallel Coiled-Coil Hexamer Formation. Authors: Spencer, R.K. / Hochbaum, A.I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w0j.cif.gz | 46.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w0j.ent.gz | 36.7 KB | Display | PDB format |
PDBx/mmJSON format | 5w0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/5w0j ftp://data.pdbj.org/pub/pdb/validation_reports/w0/5w0j | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 3438.790 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-CL / | #3: Water | ChemComp-HOH / | |
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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: 1.87 Å3/Da / Density % sol: 34.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M sodium formate pH 6.5, 35% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2016 |
Radiation | Monochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.201→40.89 Å / Num. obs: 5328 / % possible obs: 99.51 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.04 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.201→2.29 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 300 / CC1/2: 0.96 / Rpim(I) all: 0.11 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.201→40.887 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.201→40.887 Å
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Refine LS restraints |
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LS refinement shell |
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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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