+Open data
-Basic information
Entry | Database: PDB / ID: 2lkv | ||||||
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Title | Staphylococcal Nuclease PHS variant | ||||||
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 / torsion angle dynamics, simulated annealing | ||||||
Model details | closest to the average, model 1 | ||||||
Authors | Matzapetakis, M. / Pais, T.M. / Lamosa, P. / Turner, D.L. / Santos, H. | ||||||
Citation | Journal: Protein Sci. / Year: 2012 Title: Mannosylglycerate stabilizes staphylococcal nuclease with restriction of slow beta-sheet motions. Authors: Pais, T.M. / Lamosa, P. / Matzapetakis, M. / Turner, D.L. / Santos, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lkv.cif.gz | 466.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lkv.ent.gz | 387.4 KB | Display | PDB format |
PDBx/mmJSON format | 2lkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/2lkv ftp://data.pdbj.org/pub/pdb/validation_reports/lk/2lkv | 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: 16762.277 Da / Num. of mol.: 1 / Fragment: UNP residues 80-228 / Mutation: P117G,S128A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MW2 / Gene: nuc, MW0769 / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): B / 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 mM [U-13C; U-15N] SNase PHS, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 1.0 mM / Component: SNase PHS-1 / Isotopic labeling: [U-13C; U-15N] |
Sample conditions | Ionic strength: 0.060 / pH: 5.50 / Pressure: 1.00 atm / Temperature: 310.00 K |
-NMR measurement
NMR spectrometer | Type: Bruker Bruker Avance III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, simulated annealing / Software ordinal: 1 Details: Initial structures were calculated using the ATNOS-CANDID module of UNIO employing CYANA. The UNIO derived constants were introduced to CNS using the RECOORD scripts for explicit water refinement. | ||||||||||||||||||||||||||||||||||||||||
NMR constraints | Hydrogen bond constraints total count: 114 | ||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 80 / Conformers submitted total number: 10 |