+Open data
-Basic information
Entry | Database: PDB / ID: 6ovu | ||||||
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Title | Coiled-coil Trimer with Glu:3,4-difluorophenylalanine:Lys Triad | ||||||
Components | Coiled-coil Trimer with Glu:3,4-difluorophenylalanine:Lys Triad | ||||||
Keywords | DE NOVO PROTEIN / Trimer / Helix | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.101 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 | 6ovu.cif.gz | 22.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ovu.ent.gz | 16.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ovu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ovu_validation.pdf.gz | 415.1 KB | Display | wwPDB validaton report |
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Full document | 6ovu_full_validation.pdf.gz | 416.2 KB | Display | |
Data in XML | 6ovu_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | 6ovu_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/6ovu ftp://data.pdbj.org/pub/pdb/validation_reports/ov/6ovu | HTTPS FTP |
-Related structure data
Related structure data | 6os8C 6osdC 6ov9C 6ovsC 6ovvC 6q1wC 6q22C 6q25C 6u47C 6v4yC 6v50C 6v57C 6v58C 6v5gC 6v5iC 6v5jC 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 on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 3936.455 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: 1.89 Å3/Da / Density % sol: 35.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 40% PEG300, 100 mM sodium cacodylate/HCl, pH 6.5, 200 mM calcium acetate |
-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: Aug 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 2.101→16.45 Å / Num. obs: 3316 / % possible obs: 99.58 % / Redundancy: 4.6 % / CC1/2: 0.966 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.68 / Rrim(I) all: 0.168 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.101→2.176 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 2 / Num. unique obs: 334 / CC1/2: 0.72 / Rpim(I) all: 0.282 / Rrim(I) all: 0.483 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.101→16.45 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.79 Å2 / Biso mean: 28.5072 Å2 / Biso min: 13.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.101→16.45 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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