[English] 日本語
![](img/lk-miru.gif)
- PDB-4r80: Crystal Structure of a De Novo Designed Beta Sheet Protein, Cysta... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4r80 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of a De Novo Designed Beta Sheet Protein, Cystatin Fold, Northeast Structural Genomics Consortium (NESG) Target OR486 | ||||||
![]() | OR486 | ||||||
![]() | DE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG) / Target OR486 / protein engineering / denovo beta sheet design / Cystatin Fold | ||||||
Function / homology | Nuclear Transport Factor 2; Chain: A, - #630 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guan, R. / Marcos, E. / O'Connell, P. / Seetharaman, J. / Janjua, H. / Xiao, R. / Maglaqui, M. / Acton, T.B. / Everett, J.K. / Baker, D. ...Guan, R. / Marcos, E. / O'Connell, P. / Seetharaman, J. / Janjua, H. / Xiao, R. / Maglaqui, M. / Acton, T.B. / Everett, J.K. / Baker, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal Structure of an engineered protein with denovo beta sheet design, Northeast Structural Genomics Consortium (NESG) Target OR486 Authors: Guan, R. / Marcos, E. / O'Connell, P. / Seetharaman, J. / Janjua, H. / Xiao, R. / Maglaqui, M. / Acton, T.B. / Everett, J.K. / Baker, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 41.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 30.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 430.5 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 10.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
| ||||||||||||
Details | The biological molecule is unknown |
-
Components
#1: Protein | Mass: 9897.169 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.9 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), 10mg/ml. Reservoir solution:0.1 M NaH2PO4, 0.1 M Na Acetate, pH 5.5, 28% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 11, 2014 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 2.445→41.671 Å / Num. all: 5311 / Num. obs: 5311 / % possible obs: 93.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 33.87 |
Reflection shell | Resolution: 2.44→2.48 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.06 / % possible all: 42.8 |
-
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 max: 86.43 Å2 / Biso mean: 27.676 Å2 / Biso min: 6.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.445→33.818 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
|