+Open data
-Basic information
Entry | Database: PDB / ID: 4o36 | ||||||
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Title | Semisynthetic RNase S1-15-H7/11-Q10 | ||||||
Components |
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Keywords | HYDROLASE / RNase S / artificial imine reductase / S-peptide | ||||||
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: 1.22 Å | ||||||
Authors | Genz, M. / Strater, N. | ||||||
Citation | Journal: Chem.Cat.Chem / Year: 2014 Title: An Artificial Imine Reductase based on the Ribonuclease S scaffold Authors: Genz, M. / Koehler, V. / Krauss, M. / Singer, D. / Hoffmann, R. / Ward, T.R. / Strater, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o36.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o36.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 4o36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/4o36 ftp://data.pdbj.org/pub/pdb/validation_reports/o3/4o36 | HTTPS FTP |
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-Related structure data
Related structure data | 2rnsS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 1742.864 Da / Num. of mol.: 1 / Fragment: unp residues 27-41 / Mutation: K7H, R10Q, Q11H / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 | ||
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#2: Protein | Mass: 11555.981 Da / Num. of mol.: 1 / Fragment: unp residues 47-150 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 | ||
#3: Chemical | ChemComp-SO4 / | ||
#4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.03 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 100 mM sodium citrate 2.4 M ammonium sulfate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2011 |
Radiation | Monochromator: Si(311) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→38.03 Å / Num. all: 165816 / Num. obs: 32726 / Observed criterion σ(I): -3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2RNS Resolution: 1.22→29.87 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.021 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.052 / 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: 23.081 Å2
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Refinement step | Cycle: LAST / Resolution: 1.22→29.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.22→1.252 Å / Total num. of bins used: 20
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