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Open data
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Basic information
Entry | Database: PDB / ID: 6v58 | ||||||
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Title | Coiled-coil Trimer with Glu:Norleucine:Lys Triad | ||||||
![]() | Coiled-coil Trimer with Glu:Norleucine:Lys Triad | ||||||
![]() | DE NOVO PROTEIN / Trimer / Helix | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Smith, M.S. / Stern, K.L. / Billings, W.M. / Price, J.L. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 25.3 KB | Display | ![]() |
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PDB format | ![]() | 16.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422 KB | Display | ![]() |
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Full document | ![]() | 422.8 KB | Display | |
Data in XML | ![]() | 4.7 KB | Display | |
Data in CIF | ![]() | 5.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6os8C ![]() 6osdC ![]() 6ov9C ![]() 6ovsC ![]() 6ovuC ![]() 6ovvC ![]() 6q1wC ![]() 6q22C ![]() 6q25C ![]() 6u47C ![]() 6v4yC ![]() 6v50C ![]() 6v57C ![]() 6v5gC ![]() 6v5iC ![]() 6v5jC ![]() 5uxtS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 3866.458 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.02 % |
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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 |
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Diffraction source | Source: ![]() |
Detector | Type: APEX II CCD / Detector: CCD / Date: Dec 19, 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: 2.2→37.78 Å / Num. obs: 3261 / % possible obs: 99.5 % / Redundancy: 4.6 % / CC1/2: 0.977 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.051 / Rrim(I) all: 0.128 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.2→2.42 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1210 / CC1/2: 0.796 / Rpim(I) all: 0.248 / Rrim(I) all: 0.408 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5UXT Resolution: 2.201→37.78 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.57 Å2 / Biso mean: 38.0147 Å2 / Biso min: 21.12 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.201→37.78 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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