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- PDB-2f3w: solution structure of 1-110 fragment of staphylococcal nuclease i... -

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Basic information

Entry
Database: PDB / ID: 2f3w
Titlesolution structure of 1-110 fragment of staphylococcal nuclease in 2M TMAO
ComponentsThermonuclease
KeywordsHYDROLASE / OB-Fold
Function / homology
Function and homology information


micrococcal nuclease / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / nucleic acid binding / extracellular region / membrane / metal ion binding
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Thermonuclease / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing torsion angle dynamics
AuthorsLiu, D. / Xie, T. / Feng, Y. / Shan, L. / Ye, K. / Wang, J.
CitationJournal: 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
DepositionNov 22, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thermonuclease


Theoretical massNumber of molelcules
Total (without water)12,3251
Polymers12,3251
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)12 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Thermonuclease / Staphylococcal nuclease / TNase / Micrococcal nuclease


Mass: 12325.398 Da / Num. of mol.: 1 / Fragment: residues 1-110
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: A5A513*PLUS, micrococcal nuclease

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 15N-separated NOESY

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Sample preparation

DetailsContents: 1mM SNase110 fragment, 2M TMAO, 0.2M HCl, DSS, NAN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 2M TMAO, 0.2M HCl / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionClassification
XwinNMR3.5collection
Felix980processing
Felix980data analysis
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: simulated annealing torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 12

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