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- PDB-1z4h: The response regulator TorI belongs to a new family of atypical e... -

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Basic information

Entry
Database: PDB / ID: 1z4h
TitleThe response regulator TorI belongs to a new family of atypical excisionase
ComponentsTor inhibition protein
KeywordsPROTEIN BINDING / DNA BINDING PROTEIN / winged helix / reverse turn
Function / homology
Function and homology information


DNA excision / negative regulation of DNA-templated transcription initiation / provirus excision / DNA recombination / sequence-specific DNA binding / DNA binding / identical protein binding
Similarity search - Function
Recoverin; domain 1 - #160 / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Response regulator inhibitor for tor operon / Probable excisionase hkaC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / non-bonded interaction for simulated annealing, refinement in an explicit water box.
AuthorsElantak, L. / Ansaldi, M. / Guerlesquin, F. / Mejean, V. / Morelli, X.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural and genetic analyses reveal a key role in prophage excision for the TorI response regulator inhibitor
Authors: Elantak, L. / Ansaldi, M. / Guerlesquin, F. / Mejean, V. / Morelli, X.
History
DepositionMar 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: 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: 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 1.4May 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: Tor inhibition protein


Theoretical massNumber of molelcules
Total (without water)7,6931
Polymers7,6931
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)17 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Tor inhibition protein / TorI


Mass: 7692.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pETsI / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9AZ38, UniProt: Q2EES9*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D 15N-separated NOESY
1213D HNCO
1313D HNCA
141CBCA(CO)NH
151HN(CO)CA
164(H)CCH-TOCSY
1722D NOESY
1822D TOCSY
1943D 13C-separated NOESY
1103HNHA
NMR detailsText: Structure calculations were performed with ARIA 1.2 using noe's, phi angle dihedral restraints estimated from 3JHNHa and TALOS-derived dihedral angle constraints.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM TorI U-15N,13C, 50mM phosphate buffer, 90% H20, 10% D2090% H20, 10%D2O
21.5mM TorI unlabelled, 50mM phosphate buffer, 90% H20, 10% D2090% H20, 10% D20
31.5mM TorI U-15N, 50mM phosphate buffer, 90% H20, 10% D2090% H20, 10% D20
41.5mM TorI U-13C, 50mM phosphate buffer, 90% H20, 10% D2090% H20, 10% D20
Sample conditionspH: 5.9 / Pressure: ambient / Temperature: 278 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
Bruker DRXBrukerDRX5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukerprocessing
Felix2002Accelrysdata analysis
CNSARIA 1.2Brunger/Nilgesstructure solution
CNSARIA 1.2refinement
RefinementMethod: non-bonded interaction for simulated annealing, refinement in an explicit water box.
Software ordinal: 1
Details: 1341 restraints: 1173 distance restraints + 68 dihedral angle constraints from TALOS + 100 dihedral angle constraints from CSI and 3JHNHa.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 17

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