+Open data
-Basic information
Entry | Database: PDB / ID: 4o37 | ||||||
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Title | seminsynthetic RNase S1-15-3Pl-7/11 | ||||||
Components |
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Keywords | HYDROLASE / RNase A / RNase S / artificial imine reductase | ||||||
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 / direct refinement / Resolution: 1.4 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 | 4o37.cif.gz | 42.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o37.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 4o37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/4o37 ftp://data.pdbj.org/pub/pdb/validation_reports/o3/4o37 | 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: 1773.921 Da / Num. of mol.: 1 / Fragment: S-peptide / Mutation: K7-> 3Pl, Q11-> 3Pl, M13 -> Nle / 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: S-protein / Mutation: wild type / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 | ||
#3: Chemical | ChemComp-CL / | ||
#4: Chemical | #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: 2.01 Å3/Da / Density % sol: 38.95 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 100 mM sodium citrate 2.2 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: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 29, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→39.95 Å / Num. all: 129943 / Num. obs: 21691 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: direct refinement Starting model: 2RNS Resolution: 1.4→24.61 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.236 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 18.275 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→24.61 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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