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- PDB-5z2o: solution structure of G2,7,13A SMAP-18 analogue -

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Entry
Database: PDB / ID: 5z2o
Titlesolution structure of G2,7,13A SMAP-18 analogue
ComponentsG2,7,13A SMAP-18 analogue
KeywordsANTIMICROBIAL PROTEIN / STRUCTURE FROM CYANA 2.1
Biological speciesOvis aries (sheep)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsJung, B. / Lee, C.W.
CitationJournal: To Be Published
Title: solution structure of G2,7,13A SMAP-18 analogue
Authors: Jung, B. / Lee, C.W.
History
DepositionJan 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model
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

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Assembly

Deposited unit
A: G2,7,13A SMAP-18 analogue


Theoretical massNumber of molelcules
Total (without water)2,1161
Polymers2,1161
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2300 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide G2,7,13A SMAP-18 analogue


Mass: 2115.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Ovis aries (sheep)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D DQF-COSY
131isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 2mM protein solution, 10mM sodium phosphate, 50mM sodium chloride, 50 %(v/v) [U-2H] TFE, 10 %(v/v) [U-2H] H2O, trifluoroethanol/water
Label: 1H_sample / Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMprotein solutionnatural abundance1
10 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
50 % v/vTFE[U-2H]1
10 % v/vH2O[U-2H]1
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichrefinement
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 6
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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