[English] 日本語
![](img/lk-miru.gif)
- PDB-4ky3: Three-dimensional Structure of the orthorhombic crystal of comput... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4ky3 | ||||||
---|---|---|---|---|---|---|---|
Title | Three-dimensional Structure of the orthorhombic crystal of computationally designed insertion domain , Northeast Structural Genomics Consortium (NESG) Target OR327 | ||||||
![]() | designed protein OR327 | ||||||
![]() | DE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Ribosomal protein S10 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuzin, A. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Gleixner, J. / Baker, D. / Everett, J.K. / Acton, T.B. ...Kuzin, A. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Gleixner, J. / Baker, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Precise assembly of complex beta sheet topologies from de novo designed building blocks. Authors: King, I.C. / Gleixner, J. / Doyle, L. / Kuzin, A. / Hunt, J.F. / Xiao, R. / Montelione, G.T. / Stoddard, B.L. / DiMaio, F. / Baker, D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 102.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 84.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 459.5 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | monomer,19.75 kD,99.6% |
-
Components
#1: Protein | Mass: 19842.973 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21_NESG / Production host: ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.56 % |
---|---|
Crystal grow | Temperature: 277 K / pH: 4.5 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir 0.1M NaAcetate pH: 4.5 PEG 3350 25%(w/v) , microbatch under oil, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 14, 2013 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.964→30 Å / Num. obs: 20480 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 74.71 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 23.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 95.731 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.964→28.156 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|