+
Open data
-
Basic information
Entry | Database: PDB / ID: 8s96 | ||||||
---|---|---|---|---|---|---|---|
Title | RNase A-Adenosine 5'-Heptaphosphate (RNaseA.p7A) | ||||||
![]() | Ribonuclease pancreatic | ||||||
![]() | RNA BINDING PROTEIN/INHIBITOR / RNase A / oligophosphate / inhibitor / nucleoside heptaphosphate / protein-ligand complex / RNA BINDING PROTEIN-INHIBITOR complex | ||||||
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 | ![]() ![]() | ||||||
![]() | Park, G. / Cummins, C. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Pentaphosphorylation via the Anhydride of Dihydrogen Pentametaphosphate: Access to Nucleoside Hexa- and Heptaphosphates and Study of Their Interaction with Ribonuclease A. Authors: Park, G. / Wralstad, E.C. / Faginas-Lago, N. / Qian, K. / Raines, R.T. / Bistoni, G. / Cummins, C.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 79.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 48.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 8fhmC ![]() 8gc9C ![]() 8gggC ![]() 1afuS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | Mass: 827.101 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20N5O25P7 / Feature type: SUBJECT OF INVESTIGATION #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.21 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 25% PEG4000, 20 mM citrate, pH 6, crystal soaked in 50 mM ligand, 30% PEG4000, 25% glycerol, 20 mM citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: APEX II CCD / Detector: CCD / Date: Feb 13, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.544178 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→34.48 Å / Num. obs: 24657 / % possible obs: 99.9 % / Redundancy: 10.43 % / Biso Wilson estimate: 22.69 Å2 / Rpim(I) all: 0.0292 / Net I/σ(I): 3.55 |
Reflection shell | Resolution: 1.68→1.78 Å / Num. unique obs: 3862 / Rpim(I) all: 0.396 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1AFU Resolution: 1.68→34.48 Å / SU ML: 0.2042 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.616 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→34.48 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|