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- PDB-2lvl: NMR Structure the lantibiotic immunity protein SpaI -

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Basic information

Entry
Database: PDB / ID: 2lvl
TitleNMR Structure the lantibiotic immunity protein SpaI
ComponentsSpaI
KeywordsLANTIBIOTIC-BINDING-PROTEIN / lantibiotic self-immunity protein / subtilin / IMMUNE SYSTEM
Function / homologyMetal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A - #60 / Lantibiotic immunity protein Spa1, C-terminal / Lantibiotic immunity protein Spa1 C-terminal domain / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Beta Complex / Mainly Beta / SpaI
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsminimized average structure, model 1
Model type detailsminimized average
AuthorsChrist, N. / Bochmann, S. / Gottstein, D. / Duchardt-Ferner, E. / Hellmich, U.A. / Duesterhus, S. / Koetter, P. / Guentert, P. / Entian, K. / Woehnert, J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The First Structure of a Lantibiotic Immunity Protein, SpaI from Bacillus subtilis, Reveals a Novel Fold.
Authors: Christ, N.A. / Bochmann, S. / Gottstein, D. / Duchardt-Ferner, E. / Hellmich, U.A. / Dusterhus, S. / Kotter, P. / Guntert, P. / Entian, K.D. / Wohnert, J.
History
DepositionJul 6, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
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: SpaI


Theoretical massNumber of molelcules
Total (without water)14,9691
Polymers14,9691
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 SpaI


Mass: 14969.419 Da / Num. of mol.: 1 / Fragment: UNP residues 40-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: spai / Production host: Escherichia coli (E. coli) / References: UniProt: Q45403

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1242D 1H-13C HSQC aliphatic
1332D 1H-13C HSQC aromatic
1433D CBCA(CO)NH
1523D HNCO
1623D HNCA
1723D HN(CA)CB
1833D HBHA(CO)NH
1933D H(CCO)NH
11033D C(CO)NH
11143D (H)CCH-TOCSY
11243D (H)CCH-COSY
11313D HNHA
11413D 1H-15N NOESY
11533D 1H-13C NOESY aliphatic
11643D 1H-13C NOESY aliphatic
11733D 1H-13C NOESY aromatic
11823D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM sodium phosphate, 100 mM sodium chloride, 10 uM DSS, 300-400 uM [U-15N] SpaI, 90% H2O/10% D2O90% H2O/10% D2O
250 mM sodium phosphate, 100 mM sodium chloride, 10 uM DSS, 420 uM [U-13C; U-15N; U-2H] SpaI, 90% H2O/10% D2O90% H2O/10% D2O
350 mM sodium phosphate, 100 mM sodium chloride, 10 uM DSS, 300-400 uM [U-13C; U-15N] SpaI, 90% H2O/10% D2O90% H2O/10% D2O
450 mM sodium phosphate, 100 mM sodium chloride, 10 uM DSS, 300 uM [U-13C; U-15N] SpaI, 90% D2O/10% H2O90% D2O/10% H2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
50 mMsodium phosphate-11
100 mMsodium chloride-21
10 uMDSS-31
uMSpaI-4[U-15N]300-4001
50 mMsodium phosphate-52
100 mMsodium chloride-62
10 uMDSS-72
420 uMSpaI-8[U-13C; U-15N; U-2H]2
50 mMsodium phosphate-93
100 mMsodium chloride-103
10 uMDSS-113
uMSpaI-12[U-13C; U-15N]300-4003
50 mMsodium phosphate-134
100 mMsodium chloride-144
10 uMDSS-154
300 uMSpaI-16[U-13C; U-15N]4
Sample conditionsIonic strength: 100 / pH: 6.4 / Pressure: ambient / Temperature: 296 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
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CCPN_AnalysisCCPNchemical shift assignment
CCPN_AnalysisCCPNdata analysis
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
TopSpinBruker Biospinprocessing
TopSpinBruker Biospindata analysis
TopSpinBruker Biospincollection
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: WATER REFINEMENT
NMR constraintsNOE constraints total: 3246 / NOE intraresidue total count: 781 / NOE long range total count: 1301 / NOE medium range total count: 423 / NOE sequential total count: 741 / Hydrogen bond constraints total count: 36 / Protein phi angle constraints total count: 72 / Protein psi angle constraints total count: 72
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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