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Yorodumi- PDB-2m00: Solution structure of staphylococcal nuclease E43S mutant in the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2m00 | ||||||
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Title | Solution structure of staphylococcal nuclease E43S mutant in the presence of ssDNA and Cd2+ | ||||||
Components | ThermonucleaseMicrococcal nuclease | ||||||
Keywords | HYDROLASE | ||||||
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 / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | SOLUTION NMR / molecular dynamics, simulated annealing | ||||||
Authors | Xie, T. / Feng, Y. / Shan, L. / Wang, J. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2013 Title: Modeling of the [E43S]SNase-ssDNA-Cd(2+) complex: Structural insight into the action of nuclease on ssDNA. Authors: Xie, T. / Feng, Y. / Shan, L. / Wang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m00.cif.gz | 926.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m00.ent.gz | 775.8 KB | Display | PDB format |
PDBx/mmJSON format | 2m00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/2m00 ftp://data.pdbj.org/pub/pdb/validation_reports/m0/2m00 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 16776.305 Da / Num. of mol.: 1 / Mutation: E43S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MW2 / Gene: nuc, MW0769 / Plasmid: pET-3d / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NXI6, micrococcal nuclease |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.0-1.5 mM [U-13C; U-15N] protein, 50 mM sodium phosphate, 150 mM potassium chloride, 10 mM CdCl2, 0.002 w/v sodium azide, 1.5-2.25 mM 8-mer ssDNA(5'-CACTTCAT-3'), 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 210 / pH: 6.6 / Pressure: ambient / Temperature: 305 K |
-NMR measurement
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics, simulated annealing / Software ordinal: 1 | |||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |