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Yorodumi- PDB-2f0u: Crystal structure of Staphylococcal nuclease mutant V23I/L25I/I72V -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f0u | ||||||
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Title | Crystal structure of Staphylococcal nuclease mutant V23I/L25I/I72V | ||||||
Components | Staphylococcal nuclease | ||||||
Keywords | HYDROLASE / DNA HYDROLASE / RNA HYDROLASE / ENDONUCLEASE / CALCIUM / SIGNAL | ||||||
Function / homology | Function and homology information micrococcal nuclease / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / nucleic acid binding / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Lu, J.Z. / Sakon, J. / Stites, W.E. | ||||||
Citation | Journal: To be Published Title: Hydrophobic core mutants of Staphylococcal nuclease Authors: Lu, J.Z. / 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 | 2f0u.cif.gz | 42.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f0u.ent.gz | 29.6 KB | Display | PDB format |
PDBx/mmJSON format | 2f0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f0u_validation.pdf.gz | 365.2 KB | Display | wwPDB validaton report |
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Full document | 2f0u_full_validation.pdf.gz | 367.7 KB | Display | |
Data in XML | 2f0u_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | 2f0u_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/2f0u ftp://data.pdbj.org/pub/pdb/validation_reports/f0/2f0u | HTTPS FTP |
-Related structure data
Related structure data | 2f0dC 2f0eC 2f0fC 2f0gC 2f0hC 2f0iC 2f0jC 2f0kC 2f0lC 2f0mC 2f0nC 2f0oC 2f0pC 2f0qC 2f0sC 2f0tC 2f0vC 2f0wC 4h7bC 4i65C 4k8iC 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: 16843.330 Da / Num. of mol.: 1 / Mutation: V23I/L25I/I72V 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: 2.1 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50mM phosphate buffer, 45% MPD, pH 7.5, 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 RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→8 Å / Num. all: 11981 / Num. obs: 11981 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→8 Å / Num. parameters: 4912 / Num. restraintsaints: 4585 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1169.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→8 Å
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Refine LS restraints |
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