+Open data
-Basic information
Entry | Database: PDB / ID: 6nyk | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of computationally designed protein XAX_GGDQ | |||||||||
Components | Design construct XAX_GGDQ | |||||||||
Keywords | DE NOVO PROTEIN / homotrimer / helix | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Wei, K.Y. / Bick, M.J. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Computational design of closely related proteins that adopt two well-defined but structurally divergent folds. Authors: Wei, K.Y. / Moschidi, D. / Bick, M.J. / Nerli, S. / McShan, A.C. / Carter, L.P. / Huang, P.S. / Fletcher, D.A. / Sgourakis, N.G. / Boyken, S.E. / Baker, D. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6nyk.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6nyk.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 6nyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/6nyk ftp://data.pdbj.org/pub/pdb/validation_reports/ny/6nyk | HTTPS FTP |
---|
-Related structure data
Related structure data | 6nx2C 6nxmC 6ny8C 6nyeC 6nyiC 6nz1C 6nz3C 6o0cC 6o0iC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11161.817 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.08 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.0 M lithium chloride, 0.1 M MES pH 6.0, 20% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1111 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1111 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.35 Å / Num. obs: 8627 / % possible obs: 98.18 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.103 / Rrim(I) all: 0.039 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 4.228 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 821 / CC1/2: 0.187 / Rrim(I) all: 4.6 / Rsym value: 1.788 / % possible all: 97.16 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48.35 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 41.12
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 226.43 Å2 / Biso mean: 85.8214 Å2 / Biso min: 42.87 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→48.35 Å
| |||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
|