+Open data
-Basic information
Entry | Database: PDB / ID: 2eyf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Staphylococcal nuclease mutant T44V | ||||||
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: 1.8 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2eyf.cif.gz | 40.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2eyf.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 2eyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/2eyf ftp://data.pdbj.org/pub/pdb/validation_reports/ey/2eyf | HTTPS FTP |
---|
-Related structure data
Related structure data | 2exzC 2ey1C 2ey2C 2ey5C 2ey6C 2eyhC 2eyjC 2eylC 2eymC 2eyoC 2eypC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16841.355 Da / Num. of mol.: 1 / Mutation: T44V 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 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 43.6 % |
---|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
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: 1.8→8 Å / Num. all: 12712 / Num. obs: 12712 / Observed criterion σ(I): 0 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→8 Å / Num. parameters: 4558 / Num. restraintsaints: 4420 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1132 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|