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- PDB-2k5x: Chemical shift structure of COLICIN E9 DNASE domain with its cogn... -

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Basic information

Entry
Database: PDB / ID: 2k5x
TitleChemical shift structure of COLICIN E9 DNASE domain with its cognate immunity protein IM9
Components
  • Colicin-E9
  • Colicin-E9 immunity protein
KeywordsIMMUNE SYSTEM/HYDROLASE / COLICIN E9 / IMMUNITY PROTEIN IM9 / Bacteriocin immunity / Plasmid / Antibiotic / Antimicrobial / Bacteriocin / Endonuclease / Hydrolase / Metal-binding / Nuclease / Zinc / IMMUNE SYSTEM-HYDROLASE COMPLEX
Function / homology
Function and homology information


extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium / protein domain specific binding / protein-containing complex / metal ion binding
Similarity search - Function
Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain / Colicin/pyocin, DNase domain / Colicin E immunity protein / Colicin immunity protein/pyocin immunity protein / Colicin E immunity protein superfamily / Colicin immunity protein / pyocin immunity protein / Colicin/pyocin, DNase domain superfamily / Colicin/Pyocin-S2, DNase domain / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 ...Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain / Colicin/pyocin, DNase domain / Colicin E immunity protein / Colicin immunity protein/pyocin immunity protein / Colicin E immunity protein superfamily / Colicin immunity protein / pyocin immunity protein / Colicin/pyocin, DNase domain superfamily / Colicin/Pyocin-S2, DNase domain / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 / Cloacin colicin family / Colicin-like bacteriocin tRNase domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / His-Me finger superfamily / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Colicin-E9 / Colicin-E9 immunity protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsMontalvao, R.W. / Cavalli, A. / Vendruscolo, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Structure Determination of Protein-Protein Complexes Using NMR Chemical Shifts: Case of an Endonuclease Colicin-Immunity Protein Complex
Authors: Montalvao, R.W. / Cavalli, A. / Salvatella, X. / Blundell, T.L. / Vendruscolo, M.
History
DepositionJul 1, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 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: Colicin-E9 immunity protein
B: Colicin-E9


Theoretical massNumber of molelcules
Total (without water)24,7132
Polymers24,7132
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)1 / 500structures with the lowest energy
Representativelowest energy

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Components

#1: Protein Colicin-E9 immunity protein / ImmE9 / Microcin-E9 immunity protein


Mass: 9592.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Species: coli / Gene: imm, ceiE9 / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: P13479
#2: Protein Colicin-E9


Mass: 15120.021 Da / Num. of mol.: 1 / Fragment: UNP residues 450-582
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Species: coli / Gene: col, cei / Species (production host): coli / Production host: Escherichia coli (E. coli)
References: UniProt: P09883, Hydrolases; Acting on ester bonds

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 6.2 / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR softwareName: CHESHIRE / Developer: Andrea Cavalli / Classification: geometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CHESHIRE
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 1

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