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- PDB-2knj: NMR structure of microplusin a antimicrobial peptide from Rhipice... -

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Basic information

Entry
Database: PDB / ID: 2knj
TitleNMR structure of microplusin a antimicrobial peptide from Rhipicephalus (Boophilus) microplus
ComponentsMicroplusin preprotein
KeywordsANTIMICROBIAL PROTEIN / Antimicrobial peptide / Microplusin / Rhipicephalus (Boophilus) microplus
Function / homology
Function and homology information


copper chaperone activity / metal chelating activity / defense response to fungus / killing of cells of another organism / defense response to Gram-positive bacterium / iron ion binding / innate immune response / extracellular region
Similarity search - Function
DNA polymerase; domain 1 - #440 / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Antimicrobial peptide microplusin
Similarity search - Component
Biological speciesRhipicephalus microplus (southern cattle tick)
MethodSOLUTION NMR / simulated annealing
AuthorsPires, J.R. / Rezende, C.A. / Silva, F.D. / Daffre, S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure and mode of action of microplusin, a copper II-chelating antimicrobial peptide from the cattle tick Rhipicephalus (Boophilus) microplus.
Authors: Silva, F.D. / Rezende, C.A. / Rossi, D.C. / Esteves, E. / Dyszy, F.H. / Schreier, S. / Gueiros-Filho, F. / Campos, C.B. / Pires, J.R. / Daffre, S.
History
DepositionAug 26, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microplusin preprotein


Theoretical massNumber of molelcules
Total (without water)10,2221
Polymers10,2221
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Microplusin preprotein


Mass: 10222.336 Da / Num. of mol.: 1 / Fragment: UNP residues 21-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhipicephalus microplus (southern cattle tick)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q86LE5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-1H NOESY
1312D 1H-1H TOCSY
1433D 1H-15N NOESY
1533D 1H-15N TOCSY
1653D 1H-13C NOESY
1753D (H)CCH-COSY
1843D CBCA(CO)NH
1943D HN(CA)CB
11043D HBHA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM sodium chloride-1, 20 mM sodium phosphate-2, 0.95 mM microplusin-3, 90% H2O/10% D2O90% H2O/10% D2O
250 mM sodium chloride-4, 20 mM sodium phosphate-5, 0.95 mM microplusin-6, 100% D2O100% D2O
350 mM sodium chloride-7, 20 mM sodium phosphate-8, 0.52 mM [U-15N] microplusin-9, 90% H2O/10% D2O90% H2O/10% D2O
450 mM sodium chloride-10, 20 mM sodium phosphate-11, 0.35 mM [U-13C; U-15N] microplusin-12, 90% H2O/10% D2O90% H2O/10% D2O
550 mM sodium chloride-13, 20 mM sodium phosphate-14, 0.35 mM [U-13C; U-15N] microplusin-15, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium chloride-11
20 mMsodium phosphate-21
0.95 mMmicroplusin-31
50 mMsodium chloride-42
20 mMsodium phosphate-52
0.95 mMmicroplusin-62
50 mMsodium chloride-73
20 mMsodium phosphate-83
0.52 mMmicroplusin-9[U-15N]3
50 mMsodium chloride-104
20 mMsodium phosphate-114
0.35 mMmicroplusin-12[U-13C; U-15N]4
50 mMsodium chloride-135
20 mMsodium phosphate-145
0.35 mMmicroplusin-15[U-13C; U-15N]5
Sample conditionsIonic strength: 50 / pH: 5.6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesdata analysis
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
Sparky3.106Goddardpeak picking
Sparky3.106Goddarddata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinprocessing
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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