+Open data
-Basic information
Entry | Database: PDB / ID: 4g8y | ||||||
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Title | Crystal structure of Ribonuclease A in complex with 5b | ||||||
Components | Ribonuclease pancreaticPancreatic ribonuclease family | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / nuclease / Hydrolase-Hydrolase 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 / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Chatzileontiadou, D.S.M. / Kantsadi, A.L. / Leonidas, D.D. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2012 Title: Triazole pyrimidine nucleosides as inhibitors of Ribonuclease A. Synthesis, biochemical, and structural evaluation. Authors: Parmenopoulou, V. / Chatzileontiadou, D.S. / Manta, S. / Bougiatioti, S. / Maragozidis, P. / Gkaragkouni, D.N. / Kaffesaki, E. / Kantsadi, A.L. / Skamnaki, V.T. / Zographos, S.E. / ...Authors: Parmenopoulou, V. / Chatzileontiadou, D.S. / Manta, S. / Bougiatioti, S. / Maragozidis, P. / Gkaragkouni, D.N. / Kaffesaki, E. / Kantsadi, A.L. / Skamnaki, V.T. / Zographos, S.E. / Zounpoulakis, P. / Balatsos, N.A. / Komiotis, D. / Leonidas, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g8y.cif.gz | 67.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g8y.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 4g8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/4g8y ftp://data.pdbj.org/pub/pdb/validation_reports/g8/4g8y | HTTPS FTP |
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-Related structure data
Related structure data | 4g8vC 4g90C 2g8qS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: pancreas / References: UniProt: P61823, EC: 3.1.27.5 #2: Chemical | ChemComp-0FT / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.13 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG 4000, 20 mM Nacitrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54178 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Nov 21, 2011 |
Radiation | Monochromator: Cu-K / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 22087 / Num. obs: 22087 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.12 % / Biso Wilson estimate: 13.65 Å2 / Rsym value: 0.1 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Mean I/σ(I) obs: 2.8 / Num. unique all: 2588 / Rsym value: 0.441 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2G8Q Resolution: 1.8→13.884 Å / SU ML: 0.22 / σ(F): 1.37 / Phase error: 23.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.59 Å2 / ksol: 0.413 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→13.884 Å
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Refine LS restraints |
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LS refinement shell |
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