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- PDB-2hx6: Solution structure analysis of the phage T4 endoribonuclease RegB -

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Basic information

Entry
Database: PDB / ID: 2hx6
TitleSolution structure analysis of the phage T4 endoribonuclease RegB
ComponentsRibonuclease
KeywordsHYDROLASE / alpha/beta fold
Function / homologyT4 endoribonuclease RegB / T4-page Endoribonuclease RegB / nuclease activity / Hydrolases; Acting on ester bonds / Endoribonuclease RegB
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodSOLUTION NMR / mix of manual, automatic NOE assignment procedure
AuthorsOdaert, B. / Saida, F. / Uzan, M. / Bontems, F.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural and functional studies of RegB, a new member of a family of sequence-specific ribonucleases involved in mRNA inactivation on the ribosome.
Authors: Odaert, B. / Saida, F. / Aliprandi, P. / Durand, S. / Crechet, J.B. / Guerois, R. / Laalami, S. / Uzan, M. / Bontems, F.
History
DepositionAug 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 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: Ribonuclease


Theoretical massNumber of molelcules
Total (without water)17,9401
Polymers17,9401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 30structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations
Representative

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Components

#1: Protein Ribonuclease / Gp61.9


Mass: 17939.549 Da / Num. of mol.: 1 / Mutation: H48A
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: regB, 61.9 / Plasmid: pTOXR(RegB-H48A) / Production host: Escherichia coli (E. coli) / Strain (production host): BL31(DE3)
References: UniProt: P13312, Hydrolases; Acting on ester bonds

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCO
121HNCA
131HN(CO)CA
141HN(CA)CB
151CBCA(CO)NH
162(H)CCH-TOCSY
1723D 13C-separated NOESY
1833D 15N-separated NOESY
1942D NOESY
11042D TOCSY
11142D COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1Uniform labeling with 13C, 15N (U-80% 13C, U-100% 15N)90% H2O, 10% D20
2Uniform labeling with 13C, 15N (U-80% 13C, U-100% 15N)100% D2O
3Uniform labeling with 15N (U-100% 15N)90% H2O/10% D2O
4Uniform labeling with 15N (U-100% 15N)100% D2O
Sample conditionsIonic strength: 50 mM citrate, 300 mM NaCl, 20 mM DTT / pH: 6 / Pressure: ambient / Temperature: 305 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5BRUKERprocessing
Sparky3.11Goddard T.D. and Kneller D.G.data analysis
INCA1Gilquin B.structure solution
INCA1Gilquin B.refinement
RefinementMethod: mix of manual, automatic NOE assignment procedure / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 15

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