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Yorodumi- PDB-2mf2: Structural and biophysical characterization of the mRNA interfera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mf2 | ||||||
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Title | Structural and biophysical characterization of the mRNA interferase SaMazF from Staphylococcus aureus. | ||||||
Components | mRNA interferase MazF | ||||||
Keywords | HYDROLASE / CcdB/MazF fold / ribonuclease | ||||||
Function / homology | Function and homology information rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | closest to the average, model1 | ||||||
Authors | Zorzini, V. / Cheung, A. / Loris, R. / van Nuland, N.A.J. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2014 Title: Structural and biophysical characterization of Staphylococcus aureus SaMazF shows conservation of functional dynamics Authors: Zorzini, V. / Buts, L. / Sleutel, M. / Garcia-Pino, A. / Talavera, A. / Haesaerts, S. / De Greve, H. / Cheung, A. / van Nuland, N.A.J. / Loris, R. #1: Journal: Biomol.Nmr Assign. / Year: 2011 Title: 1H, 13C, and 15N backbone and side-chain chemical shift assignment of the staphylococcal MazF mRNA interferase. Authors: Zorzini, V. / Haesaerts, S. / Cheung, A. / Loris, R. / van Nuland, N.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mf2.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2mf2.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 2mf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/2mf2 ftp://data.pdbj.org/pub/pdb/validation_reports/mf/2mf2 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
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: 14821.011 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mazF, MW1992 / Plasmid: pDuet1 / Production host: Escherichia coli (E. coli) References: UniProt: Q7A0D7, UniProt: Q2FWI8*PLUS, Hydrolases; Acting on ester bonds |
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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 mM [U-99% 13C; U-99% 15N] SaMazF, 90 % H2O, 10 % D2O, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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Sample |
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Sample conditions | pH: 6.6 / Pressure: 1 atm / Temperature: 308 K |
-NMR measurement
NMR spectrometer | Type: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 / Details: Final refinement in water | ||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |