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- PDB-2m8v: Solution Structure and Activity Study of Bovicin HJ50, a Particul... -

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Basic information

Entry
Database: PDB / ID: 2m8v
TitleSolution Structure and Activity Study of Bovicin HJ50, a Particular Type AII Lantibiotic
ComponentsBovA
KeywordsANTIBIOTIC / lantibiotic
Function / homologyLantibiotic, type A, Lactobacillales-type / Type-A lantibiotic / killing of cells of another organism / defense response to bacterium / signaling receptor binding / extracellular region / Lantibiotic
Function and homology information
Biological speciesStreptococcus equinus (bacteria)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailslowest energy, model1
AuthorsZhang, J. / Feng, Y. / Wang, J. / Zhong, J.
CitationJournal: Biochem.J. / Year: 2014
Title: Type AII lantibiotic bovicin HJ50 with a rare disulfide bond: structure, structure-activity relationships and mode of action.
Authors: Zhang, J. / Feng, Y. / Teng, K. / Lin, Y. / Gao, Y. / Wang, J. / Zhong, J.
History
DepositionMay 29, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_software / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 2.0Jul 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / struct_conn
Item: _database_2.pdbx_DOI / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BovA


Theoretical massNumber of molelcules
Total (without water)3,4401
Polymers3,4401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide BovA / Bovicin HJ50


Mass: 3440.091 Da / Num. of mol.: 1 / Fragment: UNP residues 26-58
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus equinus (bacteria) / Strain: HJ50 / Gene: bovA / Production host: Escherichia coli (E. coli) / References: UniProt: Q83ZN8
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC
1212D DQF-COSY
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1522D 1H-13C HSQC
1622D 1H-1H TOCSY
1722D DQF-COSY
1822D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM BovA-1, 50 mM [U-2H] sodium acetate-2, 0.01 % DSS-3, 90% H2O/10% D2O90% H2O/10% D2O
21 mM BovA-4, 50 mM [U-2H] sodium acetate-5, 0.01 % DSS-6, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMBovA-11
50 mMsodium acetate-2[U-2H]1
0.01 %DSS-31
1 mMBovA-42
50 mMsodium acetate-5[U-2H]2
0.01 %DSS-62
Sample conditionsIonic strength: 50 / pH: 5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
FelixAccelrys Software Inc.processing
NMRViewJJohnson, One Moon Scientificchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSrefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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