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- PDB-2no8: NMR Structure analysis of the colicin immuntiy protein IM2 -

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Basic information

Entry
Database: PDB / ID: 2no8
TitleNMR Structure analysis of the colicin immuntiy protein IM2
ComponentsColicin-E2 immunity protein
KeywordsIMMUNE SYSTEM / 4 helix bundle
Function / homology
Function and homology information


bacteriocin immunity / toxic substance binding
Similarity search - Function
Colicin E immunity protein / Colicin immunity protein/pyocin immunity protein / Colicin E immunity protein superfamily / Colicin immunity protein / pyocin immunity protein / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Colicin-E2 immunity protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsMacdonald, C.J.
CitationJournal: To be Published
Title: Structural Models for non Cognate Complexes of the DNase Domain of Colicin E9 and Colicin Immunity Proteins
Authors: Boetzel, R. / Morel, B. / Macdonald, C.J. / Le Duff, C.S. / Spronk, C.A.E.M. / Bonvin, A.J.J.M. / James, R. / Kleanthous, C. / Moore, G.R.
History
DepositionOct 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3Dec 27, 2023Group: 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: Colicin-E2 immunity protein


Theoretical massNumber of molelcules
Total (without water)10,0111
Polymers10,0111
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)60 / 100lowest dihedral angle and distance violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Colicin-E2 immunity protein / ImmE2 / Microcin-E2 immunity protein


Mass: 10011.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: imm, ceiB / Plasmid: pCD01 (parent plasmid pTrc99a) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P04482

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121Aliphatic 3D 13C-separated NOESY
131Aromatic 3D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 50mM phosphate buffer NA, 95% H2O, 5% D2O / Solvent system: 95% H2O/5% D2O
Sample conditionspH: 6.2 / Pressure: 1 atm / Temperature: 298 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 INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
VNMRvariancollection
NMRPipeDelaglio F. et al.processing
XEASYBartels, C. et al.data analysis
AtnosCandidHerrmann, T. et al.data analysis
X-PLORBrunger, A.T. et al.structure solution
X-PLORBrunger, A.T. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 1958 NOE-derived distance constraints, 90 dihedral angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest dihedral angle and distance violations
Conformers calculated total number: 100 / Conformers submitted total number: 60

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