+Open data
-Basic information
Entry | Database: PDB / ID: 6v4y | ||||||
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Title | Coiled-coil Trimer with Glu:Tyr:Lys Triad with a K7A mutation | ||||||
Components | Coiled-coil Trimer with Glu:Tyr:Lys Triad with a K7A mutation | ||||||
Keywords | DE NOVO PROTEIN / Trimer / Helix | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 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 | 6v4y.cif.gz | 23.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v4y.ent.gz | 14.6 KB | Display | PDB format |
PDBx/mmJSON format | 6v4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v4y_validation.pdf.gz | 248.7 KB | Display | wwPDB validaton report |
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Full document | 6v4y_full_validation.pdf.gz | 248.7 KB | Display | |
Data in XML | 6v4y_validation.xml.gz | 1 KB | Display | |
Data in CIF | 6v4y_validation.cif.gz | 1.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/6v4y ftp://data.pdbj.org/pub/pdb/validation_reports/v4/6v4y | HTTPS FTP |
-Related structure data
Related structure data | 6os8C 6osdC 6ov9C 6ovsSC 6ovuC 6ovvC 6q1wC 6q22C 6q25C 6u47C 6v50C 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: 3529.039 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: 39.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 35% 2-ethoxyethanol, 100 mM imidazole/HCl, pH 8, 50 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: Jul 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→19.907 Å / Num. obs: 9078 / % possible obs: 99.8 % / Redundancy: 9.4 % / CC1/2: 0.913 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.052 / Rrim(I) all: 0.206 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.8501→1.9476 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 990 / CC1/2: 0.822 / Rpim(I) all: 0.261 / Rrim(I) all: 0.523 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6OVS Resolution: 1.85→19.907 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.8 Å2 / Biso mean: 23.305 Å2 / Biso min: 10.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→19.907 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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