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- PDB-2mvi: Structure of the S-glycosylated bacteriocin ASM1 -

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Basic information

Entry
Database: PDB / ID: 2mvi
TitleStructure of the S-glycosylated bacteriocin ASM1
ComponentsBacteriocin plantarican ASM1
KeywordsANTIMICROBIAL PROTEIN / glycopeptide / S-glycosylation / O-glycosylation / bacteriocin / glycocin
Function / homologykilling of cells of another organism / defense response to Gram-positive bacterium / extracellular region / Bacteriocin plantaricin ASM1
Function and homology information
Biological speciesLactobacillus plantarum (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsGoroncy, A.K. / Loo, T.S. / Koolard, A. / Patchett, M.L. / Norris, G.E.
CitationJournal: To be Published
Title: Structural characterization of the S-glycosylated bacteriocin ASM1 from Lactobacillus plantarum
Authors: Goroncy, A.K. / Loo, T.S. / Koolard, A. / Patchett, M.L. / Norris, G.E.
History
DepositionOct 6, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jun 14, 2023Group: Database references / Other / Structure summary / Category: chem_comp / database_2 / pdbx_database_status
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriocin plantarican ASM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0943
Polymers4,6511
Non-polymers4422
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Bacteriocin plantarican ASM1


Mass: 4651.206 Da / Num. of mol.: 1 / Fragment: UNP residues 22-64 / Source method: isolated from a natural source / Source: (natural) Lactobacillus plantarum (bacteria) / References: UniProt: C7G1H4
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HMBC
1412D 1H-1H TOCSY
1512D 1H-15N-HSQC-TOCSY
1612D 1H-13C-HSQC-TOCSY
1712D 1H-13C-H2BC
1812D 1H-1H NOESY

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Sample preparation

DetailsContents: 1 mM protein, 38% d3-acetonitrile, 56.8% water, 0.2% d-acetic acid, 5% D2O
Solvent system: 38% d3-acetonitrile, 56.8% water, 0.2% d-acetic acid, 5% D2O
SampleConc.: 1 mM / Component: entity-1
Sample conditionsPressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
NMRPipe2011.118.08.55Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
KUJIRA0.9843Naohiro Kobayashiprocessing
NMRViewJohnson, One Moon Scientificprocessing
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 577 / NOE long range total count: 116 / NOE medium range total count: 138 / Protein other angle constraints total count: 33 / Protein phi angle constraints total count: 17 / Protein psi angle constraints total count: 16
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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