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- PDB-2kwp: Solution structure of the aminoterminal domain of E. coli NusA -

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Basic information

Entry
Database: PDB / ID: 2kwp
TitleSolution structure of the aminoterminal domain of E. coli NusA
ComponentsTranscription elongation protein nusA
KeywordsTRANSCRIPTION / NusA
Function / homology
Function and homology information


bacterial-type RNA polymerase core enzyme binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribosome biogenesis / protein complex oligomerization / DNA-binding transcription factor activity / protein domain specific binding / nucleotide binding ...bacterial-type RNA polymerase core enzyme binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribosome biogenesis / protein complex oligomerization / DNA-binding transcription factor activity / protein domain specific binding / nucleotide binding / RNA binding / cytosol
Similarity search - Function
N Utilization Substance Protein A; Chain:P; domain 4 / NusA, N-terminal domain / Transcription termination factor NusA, C-terminal duplication / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like KH domain / Transcription termination/antitermination protein NusA, bacterial ...N Utilization Substance Protein A; Chain:P; domain 4 / NusA, N-terminal domain / Transcription termination factor NusA, C-terminal duplication / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like KH domain / Transcription termination/antitermination protein NusA, bacterial / Type-1 KH domain profile. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / K homology domain superfamily, prokaryotic type / K homology domain-like, alpha/beta / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcription termination/antitermination protein NusA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsSchweimer, K. / Jurk, M. / Roesch, P.
CitationJournal: To be Published
Title: Solution structure of the aminoterminal domain of E. coli NusA
Authors: Jurk, M. / Schweimer, K. / Roesch, P.
History
DepositionApr 15, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription elongation protein nusA


Theoretical massNumber of molelcules
Total (without water)14,8951
Polymers14,8951
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcription elongation protein nusA / N utilization substance protein A / L factor


Mass: 14894.828 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: nusA / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFF6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HNCO
1513D 1H-15N NOESY
1622D 1H-13C HSQC
1723D 1H-13C NOESY
1823D (H)CCH-TOCSY
1923D CCH-TOCSY
11023D CCH-NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4mM [U-98% 13C; U-98% 15N] protein-1, 10mM potassium phosphate-2, 50mM sodium chloride-3, 0.05mM EDTA-4, 90% H2O/10% D2O90% H2O/10% D2O
20.4mM [U-98% 13C; U-98% 15N] protein-5, 10mM potassium phosphate-6, 50mM sodium chloride-7, 0.05mM EDTA-8, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMprotein-1[U-98% 13C; U-98% 15N]1
10 mMpotassium phosphate-21
50 mMsodium chloride-31
0.05 mMEDTA-41
0.4 mMprotein-5[U-98% 13C; U-98% 15N]2
10 mMpotassium phosphate-62
50 mMsodium chloride-72
0.05 mMEDTA-82
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
NMRViewJohnson, One Moon Scientificdata analysis
XwinNMRBruker Biospincollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 20 / Representative conformer: 1

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