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- PDB-5z26: solution structure of SMAP-18 -

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Basic information

Entry
Database: PDB / ID: 5z26
Titlesolution structure of SMAP-18
ComponentsSMAP-18
KeywordsANTIMICROBIAL PROTEIN / STRUCTURE FROM CYANA 2.1
Function / homology
Function and homology information


antibacterial innate immune response / lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / extracellular space
Similarity search - Function
Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cathelicidin / Cystatin superfamily
Similarity search - Domain/homology
Cathelin-related peptide SC5
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsJung, B. / Lee, C.W.
CitationJournal: To Be Published
Title: solution structure of SMAP-18
Authors: Jung, B. / Lee, C.W.
History
DepositionDec 29, 2017Deposition 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

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SMAP-18


Theoretical massNumber of molelcules
Total (without water)2,0741
Polymers2,0741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2260 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide SMAP-18


Mass: 2073.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Ovis aries (sheep) / References: UniProt: P49928*PLUS

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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: 10 mM NA-Na,P,O,H sodium phosphate, 2.0 mM NA-C,O,N,H protein solution, 50 mM NA-Na,Cl sodium chloride, 50 % v/v [U-2H] TFE, 10 % v/v [U-2H] H2O, trifluoroethanol/water
Label: 1H_smaple / Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium phosphateNA-Na,P,O,H1
2.0 mMprotein solutionNA-C,O,N,H1
50 mMsodium chlorideNA-Na,Cl1
50 % v/vTFE[U-2H]1
10 % v/vH2O[U-2H]1
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 6 / 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
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
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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