+
Open data
-
Basic information
Entry | Database: PDB / ID: 1js0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of 3D Domain-swapped RNase A Minor Trimer | ||||||
![]() | RIBONUCLEASE A | ||||||
![]() | HYDROLASE / 3D domain swapping / RNase A | ||||||
Function / homology | ![]() pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, Y. / Gotte, G. / Libonati, M. / Eisenberg, D. | ||||||
![]() | ![]() Title: Structures of the two 3D domain-swapped RNase A trimers. Authors: Liu, Y. / Gotte, G. / Libonati, M. / Eisenberg, D. #1: ![]() Title: The Crystal Structure of a 3D Domain-swapped Dimer of RNase A at a 2.1 A Resolution Authors: Liu, Y. / Hart, P.J. / Schlunegger, M.P. / Eisenberg, D. #2: ![]() Title: A domain-swapped RNase A dimer with implications for amyloid formation Authors: Liu, Y. / Gotte, G. / Libonati, M. / Eisenberg, D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 88.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 68.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 458 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 27.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rtbS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.13 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.7 Details: PEG 10,000, amonium sulfate, pH 3.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.7 | ||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2001 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→100 Å / Num. all: 22989 / Num. obs: 22989 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.096 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 2250 / Rsym value: 0.412 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 327545 / Rmerge(I) obs: 0.096 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1RTB Resolution: 2.2→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.9 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.22 Å
| |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 10.9 % / Rfactor obs: 0.184 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.9 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.906 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.348 / Rfactor Rwork: 0.245 |