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- PDB-1jok: Averaged structure for Staphylococcal nuclease-H124L in ternary c... -

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Basic information

Entry
Database: PDB / ID: 1jok
TitleAveraged structure for Staphylococcal nuclease-H124L in ternary complex with Ca2+ and thymidine-3',5'-bisphosphate
Componentsstaphylococcal nucleaseMicrococcal nuclease
KeywordsHYDROLASE / ternary complex / beta barrel / alpha helix
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
Thermonuclease family signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / 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) ...Thermonuclease family signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / 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
THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / Distance, hydrogen bond, torsion angle constraints
Model type detailsminimized average
AuthorsWang, J. / Truckses, D.M. / Abildgaard, F. / Dzakula, Z. / Zolnai, Z. / Markley, J.L.
CitationJournal: J.Biomol.NMR / Year: 1997
Title: Solution structures of staphylococcal nuclease from multidimensional, multinuclear NMR: nuclease-H124L and its ternary complex with Ca2+ and thymidine-3',5'-bisphosphate.
Authors: Wang, J. / Truckses, D.M. / Abildgaard, F. / Dzakula, Z. / Zolnai, Z. / Markley, J.L.
History
DepositionJul 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 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: staphylococcal nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2212
Polymers16,8181
Non-polymers4021
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein staphylococcal nuclease / Micrococcal nuclease / thermonuclease / tnase / micrococcal nuclease


Mass: 16818.340 Da / Num. of mol.: 1 / Fragment: nuclease A / Mutation: H124L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pTSN2cc / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: P00644, micrococcal nuclease
#2: Chemical ChemComp-THP / THYMIDINE-3',5'-DIPHOSPHATE / Thymidine diphosphate


Type: DNA linking / Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111E-COSY
222HMQC-J
133DQF-COSY
1412D NOESY
2542D NOESY
2623D 1H-15N NOESY-HMQC
2723D HMQC-NOESY-HMQC
2852D 1H-13C HMQC
296HNCO
1101and others

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Sample preparation

Details
Solution-IDContentsSolvent system
13.5-5 mM Nuclease-H124L U-50% 2H; 300 mM KCl; D2OD2O
23.5-5 mM Nuclease-H124L U-95% 15N; 300 mM KCl; H2OH2O
33.5-5 mM Nuclease-H124L; 300 mM KCl; D2OD2O
43.5-5 mM Nuclease-H124L U-50% 2H; 300 mM KCl; H2OH2O
53.5-5 mM Nuclease-H124L U-98% 13C; 300 mM KCl; H2OH2O
63.5-5 mM Nuclease-H124L U-98% 13C U-99% 15N; 300 mM KCl; H2OH20
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1300 nM KCl 5.5 ambient 318 K
2300 nM KCl 5.1 ambient 318 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMBrukerAM5001
Bruker AMBrukerAM6002

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Processing

NMR software
NameVersionDeveloperClassification
FelixBiosym Technologies Incprocessing
X-PLOR3.1Brungerstructure solution
Insight II2.3Biosym Technologies Incstructure solution
HBPLUSMcDonald and Thorntonstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: Distance, hydrogen bond, torsion angle constraints / Software ordinal: 1
Details: 2261 constraints were used to calculate the structure. Ca2+ is bound, but coordinates for the calcium are not provided.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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