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- PDB-1nz9: Solution Structure of the N-utilization substance G (NusG) C-term... -

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Entry
Database: PDB / ID: 1nz9
TitleSolution Structure of the N-utilization substance G (NusG) C-terminal (NGC) domain from Thermus thermophilus
ComponentsTRANSCRIPTION ANTITERMINATION PROTEIN NUSG
KeywordsTRANSCRIPTION / TRANSCRIPTION ELONGATION / TERMINATION / ANTITERMINATION / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / cytosol
Similarity search - Function
: / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / SH3 type barrels. - #30 / NusG-like / Transcription termination factor nusG / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily ...: / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / SH3 type barrels. - #30 / NusG-like / Transcription termination factor nusG / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / SH3 type barrels. / KOW (Kyprides, Ouzounis, Woese) motif. / Translation protein SH3-like domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Roll / Mainly Beta
Similarity search - Domain/homology
Transcription termination/antitermination protein NusG
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsReay, P. / Yamasaki, K. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2004
Title: Structural and sequence comparisons arising from the solution structure of the transcription elongation factor NusG from Thermus thermophilus
Authors: Reay, P. / Yamasaki, K. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionFeb 17, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTION ANTITERMINATION PROTEIN NUSG


Theoretical massNumber of molelcules
Total (without water)6,3611
Polymers6,3611
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)31 / 90structures with the lowest energy, NONE WITH DISTANCE VIOLATIONS > 0.2 ANGSTROMS, NONE WITH DIHEDRAL ANGLE RESTRAINT VIOLATIONS > 2 DEGREES
RepresentativeModel #1lowest energy

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Components

#1: Protein TRANSCRIPTION ANTITERMINATION PROTEIN NUSG / N-UTILIZATION SUBSTANCE G


Mass: 6361.215 Da / Num. of mol.: 1 / Fragment: C-TERMINAL (NGC) DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: NusG / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P35872

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
123HSQC
132HMQC-J
NMR detailsText: Model 31 is the minimized average structure

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM NusG C-domain, 50mM phosphate buffer, 100mM KCL, 95% H2O, 5% D2O95% H2O/5% D2O
22mM 15N NusG C-domain, 50mM phosphate buffer, 100mM KCL, 95% H2O, 5% D2O95% H2O/5% D2O
32mM 15N NusG C-domain, 50mM phosphate buffer, 100mM KCL, 100% D2O100% D2O
Sample conditionsIonic strength: 50mM phospahte, 100mM KCl / pH: 5.5 / Pressure: ambient / Temperature: 318 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 DMXBrukerDMX5001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
ANSIG3.3Kraulisdata analysis
CNS1.1Brungerstructure solution
CNS1.1refinement
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: 566 UNAMBIGUOUS NOE DISTANCE RESTRAINTS, 52 HYDROGEN BOND RESTRAINTS, 46 HN-N DIPOLAR COUPLINGS, NO RESONANCES WERE ASSIGNED FOR ALA 127
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy, NONE WITH DISTANCE VIOLATIONS > 0.2 ANGSTROMS, NONE WITH DIHEDRAL ANGLE RESTRAINT VIOLATIONS > 2 DEGREES
Conformers calculated total number: 90 / Conformers submitted total number: 31

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