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- PDB-2jub: Solution structure of IPI* -

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Basic information

Entry
Database: PDB / ID: 2jub
TitleSolution structure of IPI*
ComponentsInternal protein I
KeywordsEndonuclease Inhibitor / IpI* / T4 phage / solution
Function / homology
Function and homology information


type IV site-specific deoxyribonuclease activity
Similarity search - Function
Ipi1, C-terminal domain / Double Stranded RNA Binding Domain - #860 / Bacteriophage T4, IpI / Bacteriophage T4, IpI C-terminal domain superfamily / Nuclease inhibitor from bacteriophage T4 / N-terminal domain of TfIIb / Double Stranded RNA Binding Domain / Single Sheet / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T4 (virus)
MethodSOLUTION NMR / distance geometry simulated annealing
Model detailsT4 phage protein IPI*
AuthorsRifat, D. / Wright, N.T. / Varney, K.M. / Weber, D.J. / Black, L.W.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Restriction endonuclease inhibitor IPI* of bacteriophage T4: a novel structure for a dedicated target.
Authors: Rifat, D. / Wright, N.T. / Varney, K.M. / Weber, D.J. / Black, L.W.
History
DepositionAug 17, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_spectrometer ...pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 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: Internal protein I


Theoretical massNumber of molelcules
Total (without water)8,0581
Polymers8,0581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Internal protein I / IpI


Mass: 8058.370 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: ipi1, ipi / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03718

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: T4 phage protein IPI*
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D H(CCO)NH
1613D C(CO)NH
1713D 1H-15N NOESY
1814D 15N-13C NOESY
1914D 13C-13C NOESY

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Sample preparation

DetailsContents: 20 mM sodium acetate, 10 % D2O, 500 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium acetate1
10 %D2O1
500 mMentity[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 20 / pH: 4.8 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, F. et al.processing
XPLOR-NIH2.9.3Schwieters, C.D. et al.refinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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