+Open data
-Basic information
Entry | Database: PDB / ID: 6v50 | ||||||
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Title | Coiled-coil Trimer with Glu:Ser:Lys Triad with K7A mutation | ||||||
Components | Coiled-coil Trimer with Glu:Ser:Lys Triad with K7A mutation | ||||||
Keywords | DE NOVO PROTEIN / Trimer / Helix | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.285 Å | ||||||
Authors | Smith, M.S. / Stern, K.L. / Billings, W.M. / Price, J.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2020 Title: Context-Dependent Stabilizing Interactions among Solvent-Exposed Residues along the Surface of a Trimeric Helix Bundle. Authors: Stern, K.L. / Smith, M.S. / Billings, W.M. / Loftus, T.J. / Conover, B.M. / Della Corte, D. / Price, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v50.cif.gz | 23.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v50.ent.gz | 14.5 KB | Display | PDB format |
PDBx/mmJSON format | 6v50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/6v50 ftp://data.pdbj.org/pub/pdb/validation_reports/v5/6v50 | HTTPS FTP |
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-Related structure data
Related structure data | 6os8C 6osdC 6ov9C 6ovsSC 6ovuC 6ovvC 6q1wC 6q22C 6q25C 6u47C 6v4yC 6v57C 6v58C 6v5gC 6v5iC 6v5jC S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 3568.031 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: 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: 2.04 Å3/Da / Density % sol: 39.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 40% PEG300, 100 mM HEPES/NaOH, pH 7.5, 200 mM sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5406 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Apr 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 2.285→19.946 Å / Num. obs: 5113 / % possible obs: 99.9 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.029 / Rrim(I) all: 0.104 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.285→2.615 Å / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 258 / CC1/2: 0.946 / Rpim(I) all: 0.135 / Rrim(I) all: 0.104 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6OVS Resolution: 2.285→19.946 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 61.48 Å2 / Biso mean: 27.252 Å2 / Biso min: 11.71 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.285→19.946 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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