+Open data
-Basic information
Entry | Database: PDB / ID: 4k8i | ||||||
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Title | Crystal Structure of Staphylococcal Nuclease mutant I92V/V99L | ||||||
Components | Thermonuclease | ||||||
Keywords | HYDROLASE / DNA hydrolase / RNA hydrolase / endonuclease | ||||||
Function / homology | Function and homology information endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / nucleic acid binding / extracellular region / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Sanders, J.M. / Latimer, E.C. / Roeser, J.R. / Janowska, K. / Sakon, J. / Stites, W.E. | ||||||
Citation | Journal: To be Published Title: Hydrophobic core mutants of Staphylococcal nuclease Authors: Sanders, J.M. / Latimer, E.C. / Roeser, J.R. / Janowska, K. / Sakon, J. / Stites, W.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k8i.cif.gz | 39.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k8i.ent.gz | 27.4 KB | Display | PDB format |
PDBx/mmJSON format | 4k8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/4k8i ftp://data.pdbj.org/pub/pdb/validation_reports/k8/4k8i | HTTPS FTP |
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-Related structure data
Related structure data | 2f0dC 2f0eC 2f0fC 2f0gC 2f0hC 2f0iC 2f0jC 2f0kC 2f0lC 2f0mC 2f0nC 2f0oC 2f0pC 2f0qC 2f0sC 2f0tC 2f0uC 2f0vC 2f0wC 4h7bC 4i65C 4k8jC C: citing same article (ref.) |
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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
#1: Protein | Mass: 15407.873 Da / Num. of mol.: 1 / Fragment: UNP Residues 89-223 / Mutation: I174V/V191L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Plasmid: pL13 / Production host: Escherichia coli (E. coli) / Strain (production host): Ar120 / References: UniProt: P00644, micrococcal nuclease |
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#2: 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: 2.29 Å3/Da / Density % sol: 46.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25mM Sodium Phosphate, MPD 35-60%, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→22.13 Å / Num. obs: 26865 / Observed criterion σ(I): 3 / Redundancy: 1.8 % / Rmerge(I) obs: 0.062 |
Reflection shell | Resolution: 1.59→1.65 Å / Redundancy: 1.03 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 0.6 / Num. unique all: 1876 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→22.12 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.867 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.205 / 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: 49.865 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→22.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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