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Yorodumi- PDB-2f3v: Solution structure of 1-110 fragment of staphylococcal nuclease w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f3v | ||||||
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Title | Solution structure of 1-110 fragment of staphylococcal nuclease with V66W mutation | ||||||
Components | ThermonucleaseMicrococcal nuclease | ||||||
Keywords | HYDROLASE / OB-Fold | ||||||
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 | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Authors | Liu, D. / Xie, T. / Feng, Y. / Shan, L. / Ye, K. / Wang, J. | ||||||
Citation | Journal: Biophys.J. / Year: 2007 Title: Folding stability and cooperativity of the three forms of 1-110 residues fragment of staphylococcal nuclease Authors: Xie, T. / Liu, D. / 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 | 2f3v.cif.gz | 420.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f3v.ent.gz | 349.2 KB | Display | PDB format |
PDBx/mmJSON format | 2f3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/2f3v ftp://data.pdbj.org/pub/pdb/validation_reports/f3/2f3v | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12412.477 Da / Num. of mol.: 1 / Fragment: Residues 1-110 / Mutation: V66W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pET3d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P00644, UniProt: A5A523*PLUS, micrococcal nuclease |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 3D 15N-separated NOESY |
-Sample preparation
Details | Contents: 2mM V66W110 fragment, 50MM ACETATE BUFFER, DSS, NAN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 50mM ACETATE BUFFER / pH: 4.9 / Pressure: ambient / Temperature: 298 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: simulated annealing, torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 12 |