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Yorodumi- PDB-3oqy: Semi-synthetic ribonuclease S: para-cyano-phenylalanine at position 8 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oqy | ||||||
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Title | Semi-synthetic ribonuclease S: para-cyano-phenylalanine at position 8 | ||||||
Components | (Ribonuclease pancreatic) x 2 | ||||||
Keywords | HYDROLASE / artificial / non-natural / vibrational / probe / nitrile / cyano / cyanophenylalanine | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.494 Å | ||||||
Authors | Fafarman, A.T. / Boxer, S.G. | ||||||
Citation | Journal: J.Phys.Chem.B / Year: 2010 Title: Nitrile bonds as infrared probes of electrostatics in ribonuclease S. Authors: Fafarman, A.T. / Boxer, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oqy.cif.gz | 66 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oqy.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 3oqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oqy_validation.pdf.gz | 454.5 KB | Display | wwPDB validaton report |
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Full document | 3oqy_full_validation.pdf.gz | 460.1 KB | Display | |
Data in XML | 3oqy_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 3oqy_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/3oqy ftp://data.pdbj.org/pub/pdb/validation_reports/oq/3oqy | HTTPS FTP |
-Related structure data
Related structure data | 3oqzC 3or0C 1rnvS 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/peptide | Mass: 1777.954 Da / Num. of mol.: 2 / Fragment: UNP residues 27-41 / Source method: obtained synthetically / Details: Made by solid phase peptide synthesis / Source: (synth.) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 #2: Protein | Mass: 11555.981 Da / Num. of mol.: 2 / Fragment: UNP residues 47-150 / Source method: isolated from a natural source / Details: Subtilisin treated RNase A / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 #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: 2.12 Å3/Da / Density % sol: 41.99 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 25% PEG 4000, 0.08M ammonium acetate, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Date: Sep 16, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.494→68.921 Å / Num. all: 36529 / Num. obs: 34995 / % possible obs: 95.8 % / Redundancy: 4.5 % / Rsym value: 0.083 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1RNV Resolution: 1.494→41.052 Å / SU ML: 0.19 / σ(F): 0.14 / 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: 49.284 Å2 / ksol: 0.375 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.494→41.052 Å
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Refine LS restraints |
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LS refinement shell |
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