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- PDB-1doq: THE C-TERMINAL DOMAIN OF THE RNA POLYMERASE ALPHA SUBUNIT FROM TH... -

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Basic information

Entry
Database: PDB / ID: 1doq
TitleTHE C-TERMINAL DOMAIN OF THE RNA POLYMERASE ALPHA SUBUNIT FROM THERMUS THERMOPHILUS
ComponentsRNA POLYMERASE ALPHA SUBUNIT
KeywordsTRANSFERASE / TRANSCRIPTION / RNA POLYMERASE / THERMUS THERMOPHILUS
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / 5' to 3' exonuclease, C-terminal subdomain / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily ...RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / 5' to 3' exonuclease, C-terminal subdomain / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, MOLECULAR DYNAMICS
Model type detailsminimized average
AuthorsWada, T. / Yamazaki, T. / Kyogoku, Y.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The structure and the characteristic DNA binding property of the C-terminal domain of the RNA polymerase alpha subunit from Thermus thermophilus.
Authors: Wada, T. / Yamazaki, T. / Kyogoku, Y.
History
DepositionDec 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA POLYMERASE ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)7,7941
Polymers7,7941
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)1 / -
Representativeminimized average structure

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Components

#1: Protein RNA POLYMERASE ALPHA SUBUNIT


Mass: 7793.891 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PET15 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Z9H6, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY.

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Sample preparation

DetailsContents: 2MM C-TERMINAL DOMAIN OF RNA POLYMERASE ALPHA SUBUNIT-15N, 13C; 20MM PHOSPHATE BUFFER, 30MM KCL; 90% H2O, 10% D2O
Sample conditionsIonic strength: 30mM KCL / pH: 6.0 / Pressure: 1 atm / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeBAX, Acollection
X-PLOR3.1BRUNGER, A. T.processing
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, MOLECULAR DYNAMICS
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON 734 NOE-DERIVED DISTANCE CONSTRAINTS, 43 DIHEDRAL ANGLE RESTRAINTS AND 38 DISTANCE RESTRAINTS FROM HYDROGEN BONDS.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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