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- PDB-2mt4: Solution structure of the N-terminal domain of NUSA from B. Subtilis -

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Basic information

Entry
Database: PDB / ID: 2mt4
TitleSolution structure of the N-terminal domain of NUSA from B. Subtilis
ComponentsTranscription termination/antitermination protein NusA
KeywordsTRANSCRIPTION / Transcription factor / NUSA / RNA Polymerase
Function / homology
Function and homology information


transcription antitermination / DNA-templated transcription termination / DNA-binding transcription factor activity / RNA binding / cytosol
Similarity search - Function
N Utilization Substance Protein A; Chain:P; domain 4 / NusA, N-terminal domain / 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 / RNA-binding domain, S1 ...N Utilization Substance Protein A; Chain:P; domain 4 / NusA, N-terminal domain / 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 / RNA-binding domain, S1 / Type-1 KH domain profile. / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / K Homology domain / K homology RNA-binding 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 speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / distance geometry
AuthorsMobli, M. / Lewis, P.J.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: RNA polymerase-induced remodelling of NusA produces a pause enhancement complex.
Authors: Ma, C. / Mobli, M. / Yang, X. / Keller, A.N. / King, G.F. / Lewis, P.J.
History
DepositionAug 12, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Apr 1, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription termination/antitermination protein NusA


Theoretical massNumber of molelcules
Total (without water)14,0201
Polymers14,0201
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)20 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcription termination/antitermination protein NusA


Mass: 14019.858 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-124)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: nusA, BSU16600 / Plasmid: pETMCSIII / Production host: Escherichia coli (E. coli) / References: UniProt: P32727

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HBHA(CO)NH
1513D (H)CCH-TOCSY
1613D 1H-15N NOESY
1713D 1H-13C NOESY aliphatic
1813D 1H-13C NOESY aromatic
1913D HN(CA)CB
11013D CBCA(CO)NH
11113D HN(CA)CO
NMR detailsText: All 3D non-noesy data acquired with non-uniform sampling and processed using Maximum Entropy reconstruction

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Sample preparation

DetailsContents: 400 uM [U-99% 13C; U-99% 15N] NTD-NUSA, 10 mM HEPES, 150 mM sodium chloride, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMNTD-NUSA-1[U-99% 13C; U-99% 15N]1
10 mMHEPES-21
150 mMsodium chloride-31
Sample conditionsIonic strength: 0.16 / pH: 7.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
TopSpin3.1Bruker Biospincollection
Rowland_NMR_Toolkit3J. C. Hoch & A. S. Sternprocessing
TALOS+Cornilescu, Delaglio and Baxdata analysis
CCPNMR2.2CCPNpeak picking
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: distance geometry / Software ordinal: 1 / Details: AUTOMATED NOE ASSIGNMENT PROTOCOL
NMR constraintsNOE constraints total: 2407 / NOE intraresidue total count: 567 / NOE long range total count: 672 / NOE medium range total count: 541 / NOE sequential total count: 627 / Protein phi angle constraints total count: 114 / Protein psi angle constraints total count: 116
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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