+Open data
-Basic information
Entry | Database: PDB / ID: 1o0m | ||||||
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Title | Ribonuclease A in complex with uridine-2'-phosphate | ||||||
Components | Ribonuclease pancreaticPancreatic ribonuclease family | ||||||
Keywords | HYDROLASE / Ribonuclease | ||||||
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: 1.5 Å | ||||||
Authors | Leonidas, D.D. / Oikonomakos, N.G. / Chrysina, E.D. / Kosmopoulou, M.N. / Vlassi, M. | ||||||
Citation | Journal: PROTEIN SCI. / Year: 2003 Title: High-resolution crystal structures of ribonuclease A complexed with adenylic and uridylic nucleotide inhibitors. Implications for structure-based design of ribonucleolytic inhibitors Authors: Leonidas, D.D. / Chavali, G.B. / Oikonomakos, N.G. / Chrysina, E.D. / Kosmopoulou, M.N. / Vlassi, M. / Frankling, C. / Acharya, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o0m.cif.gz | 71.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o0m.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 1o0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/1o0m ftp://data.pdbj.org/pub/pdb/validation_reports/o0/1o0m | HTTPS FTP |
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-Related structure data
Related structure data | 1o0fC 1o0hC 1o0nC 1o0oC 1afuS 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 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 / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 #2: Chemical | #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: 1.8 Å3/Da / Density % sol: 31.17 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20mM SODIUM CITRATE BUFFER, 20% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / Details: Leonidas, D.D., (1997) Biochemistry, 36, 5578. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 10, 2000 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 37206 / Num. obs: 37206 / % possible obs: 98.3 % / Observed criterion σ(F): 0.1 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 21.3 Å2 / Rsym value: 0.052 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.5→1.55 Å / Num. unique all: 3586 / Rsym value: 0.39 / % possible all: 95.6 |
Reflection | *PLUS Num. measured all: 278544 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 95.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1AFU Resolution: 1.5→23.57 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1004066.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.001 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.3939 Å2 / ksol: 0.36897 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→23.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.5 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.24 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.55 Å |