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Open data
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Basic information
Entry | Database: PDB / ID: 8gc9 | ||||||
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Title | RNase A-Uridine 5'-Heptaphosphate (RNase A.p7U) | ||||||
![]() | Ribonuclease pancreatic | ||||||
![]() | RNA BINDING PROTEIN / 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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81 KB | Display | ![]() |
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PDB format | ![]() | 49.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8fhmC ![]() 8gggC ![]() 8s96C ![]() 1afuS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Fragment: UNP residues 27-150 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | Type: RNA linking / Mass: 804.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19N2O27P7 / Feature type: SUBJECT OF INVESTIGATION #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.41 % |
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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 |
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Diffraction source | Source: ![]() |
Detector | Type: APEX II CCD / Detector: CCD / Date: Jan 9, 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: 1.78→34.37 Å / Num. obs: 22245 / % possible obs: 99.9 % / Redundancy: 11.75 % / Biso Wilson estimate: 23.41 Å2 / Rpim(I) all: 0.0301 / Net I/σ(I): 8.05 |
Reflection shell | Resolution: 1.85→1.916 Å / Num. unique obs: 1729 / Rpim(I) all: 0.3316 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1AFU Resolution: 1.85→34.34 Å / SU ML: 0.2669 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9455 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→34.34 Å
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Refine LS restraints |
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LS refinement shell |
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