+Open data
-Basic information
Entry | Database: PDB / ID: 6v57 | ||||||
---|---|---|---|---|---|---|---|
Title | Coiled-coil Trimer with Glu:Norvaline:Lys Triad | ||||||
Components | Coiled-coil Trimer with Glu:Norvaline:Lys Triad | ||||||
Keywords | DE NOVO PROTEIN / Trimer / Helix | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.696 Å | ||||||
Authors | Smith, M.S. / Stern, K.L. / Billings, W.M. / Price, J.L. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6v57.cif.gz | 28.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6v57.ent.gz | 18.4 KB | Display | PDB format |
PDBx/mmJSON format | 6v57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v57_validation.pdf.gz | 410.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6v57_full_validation.pdf.gz | 410.7 KB | Display | |
Data in XML | 6v57_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 6v57_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/6v57 ftp://data.pdbj.org/pub/pdb/validation_reports/v5/6v57 | HTTPS FTP |
-Related structure data
Related structure data | 6os8C 6osdC 6ov9C 6ovsC 6ovuC 6ovvC 6q1wC 6q22C 6q25C 6u47C 6v4yC 6v50C 6v58C 6v5gC 6v5iC 6v5jC 5uxtS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein/peptide | Mass: 3852.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.87 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 40% v/v PEG600, 100 mM sodium citrate tribasic/citric acid, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5406 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Nov 27, 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: 1.696→19.16 Å / Num. obs: 6357 / % possible obs: 99.8 % / Redundancy: 7.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.036 / Rrim(I) all: 0.111 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.696→1.7641 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1233 / CC1/2: 0.91 / Rpim(I) all: 0.174 / Rrim(I) all: 0.383 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5UXT Resolution: 1.696→19.16 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 21.15
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 41.34 Å2 / Biso mean: 15.2013 Å2 / Biso min: 3.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.696→19.16 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|