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- PDB-2mc5: A bacteriophage transcription regulator inhibits bacterial transc... -

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Basic information

Entry
Database: PDB / ID: 2mc5
TitleA bacteriophage transcription regulator inhibits bacterial transcription initiation by -factor displacement
Components45L
KeywordsPROTEIN BINDING / p7 / RNAP / sigma factor
Function / homologyDouble Stranded RNA Binding Domain - #560 / : / Xanthomonas phage Xp10 Transcription regulator P7 / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / RNA polymerase inhibitor p7
Function and homology information
Biological speciesXanthomonas phage Xp10 (virus)
MethodSOLUTION NMR / distance geometry, simulated annealing
Model detailslowest energy, model1
AuthorsLiu, B. / Shadrin, A. / Sheppard, C. / Xu, Y. / Severinov, K. / Matthews, S. / Wigneshweraraj, S.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: A bacteriophage transcription regulator inhibits bacterial transcription initiation by sigma-factor displacement.
Authors: Liu, B. / Shadrin, A. / Sheppard, C. / Mekler, V. / Xu, Y. / Severinov, K. / Matthews, S. / Wigneshweraraj, S.
History
DepositionAug 14, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2May 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: 45L


Theoretical massNumber of molelcules
Total (without water)8,1891
Polymers8,1891
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)1 / 1all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein 45L / RNA polymerase inhibitor p7


Mass: 8188.970 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas phage Xp10 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LTJ5

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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 HNCO
1413D HNCA
1513D 1H-15N NOESY
1613D HN(CA)CB
1713D 1H-13C NOESY
1813D HBHA(CO)NH
1913D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 5 mM sodium chloride, 5 mM potassium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
5 mMsodium chloride-11
5 mMpotassium phosphate-21
Sample conditionsIonic strength: 10 / pH: 8.7 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 1 / Conformers submitted total number: 1

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