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- PDB-6k50: Solution structure of plectasin derivative NZ2114 -

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Basic information

Entry
Database: PDB / ID: 6k50
TitleSolution structure of plectasin derivative NZ2114
ComponentsPLECTASIN DERIVATIVE NZ2114
KeywordsANTIBIOTIC / plectasin derivative / antibacterial activity
Function / homology
Function and homology information


potassium channel regulator activity / toxin activity / defense response to bacterium / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Arthropod defensin / Invertebrate defensins family profile. / Defensin, invertebrate/fungal / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Fungal defensin plectasin
Similarity search - Component
Biological speciesPseudoplectania nigrella (fungus)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, J.H. / Mao, R.Y. / Liu, X.H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31772640 China
National Natural Science Foundation of China31570061 China
CitationJournal: To Be Published
Title: Solution structure of plectasin derivative NZ2114
Authors: Wang, J.H. / Liu, X.H. / Mao, R.Y.
History
DepositionMay 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLECTASIN DERIVATIVE NZ2114


Theoretical massNumber of molelcules
Total (without water)4,4251
Polymers4,4251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2770 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide PLECTASIN DERIVATIVE NZ2114


Mass: 4425.066 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudoplectania nigrella (fungus) / References: UniProt: Q53I06*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-15N HSQC
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-13C HSQC
141isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 2 mM NZ2114, 90% H2O/10% D2O / Label: sample_1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM / Component: NZ2114 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 mM / Label: condition_1 / pH: 4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent DD2 / Manufacturer: Agilent / Model: DD2 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger A. T. et.al.refinement
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIA2.1Linge, O'Donoghue and Nilgesstructure calculation
CcpNMR2.4CCPNdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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