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- PDB-2mf2: Structural and biophysical characterization of the mRNA interfera... -

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Basic information

Entry
Database: PDB / ID: 2mf2
TitleStructural and biophysical characterization of the mRNA interferase SaMazF from Staphylococcus aureus.
ComponentsmRNA interferase MazF
KeywordsHYDROLASE / CcdB/MazF fold / ribonuclease
Function / homology
Function and homology information


rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding
Similarity search - Function
SH3 type barrels. - #110 / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Endoribonuclease MazF / Endoribonuclease MazF
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsZorzini, 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
DepositionOct 3, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA interferase MazF
B: mRNA interferase MazF


Theoretical massNumber of molelcules
Total (without water)29,6422
Polymers29,6422
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein mRNA interferase MazF / Endoribonuclease MazF / Toxin MazF


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] SaMazF, 90 % H2O, 10 % D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSaMazF-1[U-99% 13C; U-99% 15N]1
90 %H2O-21
10 %D2O-31
Sample conditionspH: 6.6 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
RECOORD, _CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Final refinement in water
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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