+Open data
-Basic information
Entry | Database: PDB / ID: 8fhm | ||||||
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Title | RNase A-Uridine 5'-Hexaphosphate (RNaseA.p6U) | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | RNA BINDING PROTEIN/INHIBITOR / RNase A / oligophosphate / inhibitor / nucleoside hexaphosphate / protein-ligan complex / RNA BINDING PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SOLUTION SCATTERING / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Park, G. / Cummins, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Cent.Sci. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fhm.cif.gz | 200.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fhm.ent.gz | 134.8 KB | Display | PDB format |
PDBx/mmJSON format | 8fhm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/8fhm ftp://data.pdbj.org/pub/pdb/validation_reports/fh/8fhm | HTTPS FTP |
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-Related structure data
Related structure data | 8gc9C 8gggC 8s96C 1afuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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 / Source method: isolated from a natural source / Details: Chain C U6F U6F U6F / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, pancreatic ribonuclease #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.06 % |
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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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.544178 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Oct 23, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.544178 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→30.93 Å / Num. obs: 22299 / % possible obs: 99.29 % / Redundancy: 17.13 % / Biso Wilson estimate: 17.55 Å2 / Rsym value: 0.05 / Net I/σ(I): 3.13 |
Reflection shell | Resolution: 1.79→1.86 Å / Num. unique obs: 22299 / Rsym value: 0.05 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1AFU Resolution: 1.79→30.93 Å / SU ML: 0.214 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7391 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: 25.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→30.93 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 20.8943519672 Å / Origin y: -0.591650368591 Å / Origin z: 21.2729051685 Å
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Refinement TLS group | Selection details: all |