+Open data
-Basic information
Entry | Database: PDB / ID: 2eyj | ||||||
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Title | Crystal structure of Staphylococcal nuclease mutant T62V | ||||||
Components | Staphylococcal nucleaseMicrococcal nuclease | ||||||
Keywords | HYDROLASE / DNA HYDROLASE / RNA HYDROLASE / ENDONUCLEASE / CALCIUM / SIGNAL | ||||||
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 Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Lu, J.Z. / Sakon, J. / Stites, W.E. | ||||||
Citation | Journal: To be Published Title: Threonine 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 | 2eyj.cif.gz | 41.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eyj.ent.gz | 28.8 KB | Display | PDB format |
PDBx/mmJSON format | 2eyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/2eyj ftp://data.pdbj.org/pub/pdb/validation_reports/ey/2eyj | HTTPS FTP |
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-Related structure data
Related structure data | 2exzC 2ey1C 2ey2C 2ey5C 2ey6C 2eyfC 2eyhC 2eylC 2eymC 2eyoC 2eypC 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: 16841.355 Da / Num. of mol.: 1 / Mutation: T62V 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: 2.06 Å3/Da / Density % sol: 43.6 % |
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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: 1.85→8 Å / Num. all: 10960 / Num. obs: 10960 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→6 Å / Num. parameters: 4771 / Num. restraintsaints: 4581 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 8 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1160 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→6 Å
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Refine LS restraints |
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