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- PDB-1tdp: NMR solution structure of the carnobacteriocin B2 immunity protein -

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Basic information

Entry
Database: PDB / ID: 1tdp
TitleNMR solution structure of the carnobacteriocin B2 immunity protein
Componentscarnobacteriocin B2 immunity protein
KeywordsANTIMICROBIAL PROTEIN / four-helix bundle
Function / homology
Function and homology information


bacteriocin immunity / plasma membrane / cytoplasm
Similarity search - Function
Ta0600-like / Ta0600-like superfamily / Bacteriocin immunity protein family / de novo design (two linked rop proteins) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative carnobacteriocin-B2 immunity protein
Similarity search - Component
Biological speciesCarnobacterium maltaromaticum (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsSprules, T. / Kawulka, K.E. / Vederas, J.C.
CitationJournal: Biochemistry / Year: 2004
Title: NMR Solution Structure of ImB2, a Protein Conferring Immunity to Antimicrobial Activity of the Type IIa Bacteriocin, Carnobacteriocin B2
Authors: Sprules, T. / Kawulka, K.E. / Vederas, J.C.
History
DepositionMay 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: carnobacteriocin B2 immunity protein


Theoretical massNumber of molelcules
Total (without water)12,6811
Polymers12,6811
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)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein carnobacteriocin B2 immunity protein / Carnocin CP52 immunity protein


Mass: 12680.632 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carnobacterium maltaromaticum (bacteria)
Gene: cbiB2 / Plasmid: pMALc / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38582

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
1323D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM CbiB2 U-15N; 20 mM sodium phosphate buffer; 25 mM NaCl; 90% H2O, 10%D2O90% H2O/10% D2O
20.8 mM CbiB2 U-15N,13C; 20 mM sodium phosphate buffer; 25 mM NaCl; 100% D2O100% D2O
Sample conditionsIonic strength: 20 mM sodium phosphate; 25 mM NaCl / pH: 6.6 / Pressure: ambient / Temperature: 288 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Ccollection
NMRPipe2.2Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A.processing
NMRView5Johnson, B. A., and Blevins, R. A.data analysis
CNS1.1Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., and Warren, G.L.structure solution
CNS1.1Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R. J., Rice, L.M., Simonson, T., and Warren, G.L.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures are based on 2118 NOE-derived distance restraints, 84 hydrogen bonds and 130 dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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