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- PDB-2n32: NMR solution structure of the N-terminal domain of NisI, a lipopr... -

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Basic information

Entry
Database: PDB / ID: 2n32
TitleNMR solution structure of the N-terminal domain of NisI, a lipoprotein from Lactococcus lactis which confers immunity against nisin
ComponentsNisin immunity protein
KeywordsLANTIBIOTIC-BINDING PROTEIN / lantibiotic self-immunity protein / IMMUNE SYSTEM
Function / homologyLantibiotic immunity protein Spa1, C-terminal / Lantibiotic immunity protein Spa1 C-terminal domain / bacteriocin immunity / Prokaryotic membrane lipoprotein lipid attachment site profile. / plasma membrane / Nisin immunity protein
Function and homology information
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodSOLUTION NMR / torsion angle dynamics, water refinement
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsHacker, C. / Christ, N.A. / Korn, S. / Duchardt-Ferner, E. / Hellmich, U.A. / Duesterhus, S. / Koetter, P. / Entian, K. / Woehnert, J.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Solution Structure of the Lantibiotic Immunity Protein NisI and Its Interactions with Nisin.
Authors: Hacker, C. / Christ, N.A. / Duchardt-Ferner, E. / Korn, S. / Gobl, C. / Berninger, L. / Dusterhus, S. / Hellmich, U.A. / Madl, T. / Kotter, P. / Entian, K.D. / Wohnert, J.
History
DepositionMay 21, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 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

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Assembly

Deposited unit
A: Nisin immunity protein


Theoretical massNumber of molelcules
Total (without water)12,6941
Polymers12,6941
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 / 100target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein Nisin immunity protein


Mass: 12694.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Gene: nisI / Production host: Escherichia coli (E. coli) / References: UniProt: P42708

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1423D CBCA(CO)NH
1523D HNCO
1623D HN(CA)CB
1723D HBHA(CO)NH
1823D H(CCO)NH
1923D C(CO)NH
11013D 1H-15N NOESY
11123D 1H-13C NOESY aliphatic
11223D 1H-13C NOESY aromatic
11323D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM sodium phosphate, 100 mM sodium chloride, 30 uM DSS, 400 uM [U-15N] NisI2, 10 % D2O, 90 % H2O, 90% H2O/10% D2O90% H2O/10% D2O
250 mM sodium phosphate, 100 mM sodium chloride, 30 uM DSS, 400 uM [U-13C; U-15N] NisI2, 10 % D2O, 90 % H2O, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate-11
100 mMsodium chloride-21
30 uMDSS-31
400 uMNisI2-110-4[U-15N]1
10 %D2O-51
90 %H2O-61
50 mMsodium phosphate-72
100 mMsodium chloride-82
30 uMDSS-92
400 uMNisI2-110-10[U-13C; U-15N]2
10 %D2O-112
90 %H2O-122
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE9504
Bruker AvanceBrukerAVANCE9005

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Processing

NMR software
NameDeveloperClassification
CCPN_AnalysisCCPNchemical shift assignment
CCPN_AnalysisCCPNdata analysis
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
TopSpinBruker Biospincollection
TopSpinBruker Biospindata analysis
TopSpinBruker Biospinprocessing
TopSpinBruker Biospinrefinement
OPALLuginbuhl, Guntert, Billeter and Wuthrichcollection
OPALLuginbuhl, Guntert, Billeter and Wuthrichdata analysis
OPALLuginbuhl, Guntert, Billeter and Wuthrichprocessing
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, water refinement / Software ordinal: 1
NMR constraintsNOE constraints total: 2336 / NOE intraresidue total count: 526 / NOE long range total count: 904 / NOE medium range total count: 290 / NOE sequential total count: 616 / Protein phi angle constraints total count: 78 / Protein psi angle constraints total count: 78
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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