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- PDB-2krc: Solution structure of the N-terminal domain of Bacillus subtilis ... -

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Basic information

Entry
Database: PDB / ID: 2krc
TitleSolution structure of the N-terminal domain of Bacillus subtilis delta subunit of RNA polymerase
ComponentsDNA-directed RNA polymerase subunit deltaPolymerase
KeywordsTRANSCRIPTION / RNA polymerase / delta subunit / gram-positive bacteria / DNA-directed RNA polymerase / Nucleotidyltransferase / Transferase
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 (bacteria)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsMotackova, V. / Sanderova, H. / Zidek, L. / Novacek, J. / Padrta, P. / Svenkova, A. / Jonak, J. / Krasny, L. / Sklenar, V.
CitationJournal: Proteins / Year: 2010
Title: Solution structure of the N-terminal domain of Bacillus subtilis delta subunit of RNA polymerase and its classification based on structural homologs
Authors: Motackova, V. / Sanderova, H. / Zidek, L. / Novacek, J. / Padrta, P. / Svenkova, A. / Korelusova, J. / Jonak, J. / Krasny, L. / Sklenar, V.
History
DepositionDec 16, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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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)11,7691
Polymers11,7691
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 11769.083 Da / Num. of mol.: 1 / Fragment: residues 2-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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
1212D 1H-13C HMQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCA
1613D HN(CO)CA
1713D HNCO
1813D HNHA
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY
1121(HB)CB(CGCD)HD
11322D 1H-15N IPAP
11422D HN[C]-S3E
11522D (H)CACO-IPAP
11622D 13C-coupled 1H-13C HSQC
11732D 1H-15N IPAP
11832D HN[C]-S3E
11932D (H)CACO-IPAP
12032D 13C-coupled 1H-13C HSQC
12112D 13C-detected CON
12222D 13C-detected CON
12312D 1H-15N IPAP
12412D HN[C]-S3E
12512D (H)CACO-IPAP
12612D 13C-coupled 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
110 mM sodium chloride-1, 50 uM sodium azide-2, 20 mM phosphate buffer-3, 90% H2O/10% D2O90% H2O/10% D2O
210 mM sodium chloride-4, 50 uM sodium azide-5, 20 mM phosphate buffer-6, 14.29 mg/mL filamentous Pf1 bacteriophage-7, 90% H2O/10% D2O90% H2O/10% D2O
310 mM sodium chloride-8, 50 uM sodium azide-9, 20 mM phosphate buffer-10, 5 % polyacrylamide gel-11, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
10 mMsodium chloride-11
50 uMsodium azide-21
20 mMphosphate buffer-31
10 mMsodium chloride-42
50 uMsodium azide-52
20 mMphosphate buffer-62
14.29 mg/mLfilamentous Pf1 bacteriophage-72
10 mMsodium chloride-83
50 uMsodium azide-93
20 mMphosphate buffer-103
5 %polyacrylamide gel-113
Sample conditionsIonic strength: 10 / pH: 6.6 / Pressure: 1 atm / Temperature: 301 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDraw3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.111Goddardchemical shift assignment
Sparky3.111Goddardpeak picking
ARIA2.1Linge, O'Donoghue and Nilgesnoe assignment
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLORBrungerrefinement
S3EPYPetr Novakdipolar coupling determination
S3EPYPetr Novakpeak picking
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2341 / NOE intraresidue total count: 734 / NOE long range total count: 544 / NOE medium range total count: 564 / NOE sequential total count: 499 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 66 / Protein psi angle constraints total count: 66
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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