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- PDB-2m4k: Solution structure of the delta subunit of RNA polymerase from Ba... -

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Basic information

Entry
Database: PDB / ID: 2m4k
TitleSolution structure of the delta subunit of RNA polymerase from Bacillus subtilis
ComponentsDNA-directed RNA polymerase subunit deltaPolymerase
KeywordsTRANSFERASE / delta subunit / RNA polymerase
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-templated transcription / regulation of DNA-templated transcription
Similarity search - Function
RNA polymerase, subunit delta, N-terminal domain / DNA-directed RNA polymerase subunit delta / DNA-directed RNA polymerase subunit delta, N-terminal domain superfamily / ASXL, HARE-HTH domain / HB1, ASXL, restriction endonuclease HTH domain / HARE-type HTH domain profile. / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit delta
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailsfewest violations, model 1
AuthorsPapouskova, V. / Novacek, J. / Kaderavek, P. / Zidek, L. / Rabatinova, A. / Sanderova, H. / Krasny, L. / Sklenar, V.
CitationJournal: Chembiochem / Year: 2013
Title: Structural Study of the Partially Disordered Full-Length delta Subunit of RNA Polymerase from Bacillus subtilis.
Authors: Papouskova, V. / Kaderavek, P. / Otrusinova, O. / Rabatinova, A. / Sanderova, H. / Novacek, J. / Krasny, L. / Sklenar, V. / Zidek, L.
History
DepositionFeb 7, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Structure summary
Revision 1.2Jun 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 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit delta


Theoretical massNumber of molelcules
Total (without water)20,2871
Polymers20,2871
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein DNA-directed RNA polymerase subunit delta / Polymerase / RNAP delta factor


Mass: 20286.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: rpoE, BSU37160 / Production host: Escherichia coli (E. coli) / References: UniProt: P12464

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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 CBCA(CO)NH
1313D HN(CA)CB
1413D HNCA
1513D HN(CO)CA
1613D HNCO
1713D (H)CCH-TOCSY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic
11013D 1H-15N NOESY
11112D CON
11213D CBCACON
11313D CBCANCO
11413D HNCO
11515D HN CA CONH
11615D HabCabCONH
11715D H CCtocsy CONH
11812D 13C-coupled 1H-13C HSQC

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Sample preparation

DetailsContents: 10 % [U-100% 2H] D2O, 10 mM sodium chloride, 50 uM sodium azide, 20 mM sodium phosphate, 90 % H2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 %D2O-1[U-100% 2H]1
10 mMsodium chloride-21
50 uMsodium azide-31
20 mMsodium phosphate-41
90 %H2O-51
Sample conditionsIonic strength: 10 / pH: 6.6 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian Uniform NMR SystemVarianUniform NMR System7002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CINGVuister GWvalidation
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2520 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 64 / Protein psi angle constraints total count: 64
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20

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