+Open data
-Basic information
Entry | Database: PDB / ID: 3dxh | ||||||
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Title | Ribonuclease A uridine 5' diphosphate complex | ||||||
Components | Ribonuclease pancreaticPancreatic ribonuclease family | ||||||
Keywords | HYDROLASE / RIBONUCLEASE / ENDONUCLEASE / NUCLEOTIDE INHIBITOR / Glycation / Glycoprotein / Nuclease / Secreted | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å | ||||||
Authors | Tsirkone, V.G. / Dossi, K. / Leonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G. / Kontou, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Inhibitor design to Ribonuclease A: The binding of two 5'phosphate uridine analogues Authors: Tsirkone, V.G. / Dossi, K. / Drakou, C. / Zographos, S.E. / Kontou, M. / 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 | 3dxh.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dxh.ent.gz | 99.2 KB | Display | PDB format |
PDBx/mmJSON format | 3dxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/3dxh ftp://data.pdbj.org/pub/pdb/validation_reports/dx/3dxh | HTTPS FTP |
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-Related structure data
Related structure data | 3dxgC 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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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) / Tissue: pancreas / References: UniProt: P61823, EC: 3.1.27.5 #2: Chemical | ChemComp-UDP / #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: 2.13 Å3/Da / Density % sol: 42.3 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 4000, sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.0448 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 17, 2007 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0448 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. all: 45026 / Num. obs: 42757 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 14.5 Å2 / Rsym value: 0.044 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 8.2 / Num. unique all: 2290 / Rsym value: 0.111 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 2G8Q Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.152 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.566 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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