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- PDB-2auj: Structure of Thermus aquaticus RNA polymerase beta'-subunit insert -

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Basic information

Entry
Database: PDB / ID: 2auj
TitleStructure of Thermus aquaticus RNA polymerase beta'-subunit insert
ComponentsDNA-directed RNA polymerase beta' chain
KeywordsTRANSFERASE / sandwich-barrel hybrid motif
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding
Similarity search - Function
: / DNA-directed RNA polymerase subunit beta', hybrid domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 ...: / DNA-directed RNA polymerase subunit beta', hybrid domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit beta'
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / combination of molecular replacement, SAD / Resolution: 2.7 Å
AuthorsChlenov, M. / Masuda, S. / Murakami, K.S. / Nikiforov, V. / Darst, S.A. / Mustaev, A.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structure and Function of Lineage-specific Sequence Insertions in the Bacterial RNA Polymerase beta' Subunit
Authors: Chlenov, M. / Masuda, S. / Murakami, K.S. / Nikiforov, V. / Darst, S.A. / Mustaev, A.
History
DepositionAug 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: DNA-directed RNA polymerase beta' chain


Theoretical massNumber of molelcules
Total (without water)34,4891
Polymers34,4891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.724, 53.649, 69.693
Angle α, β, γ (deg.)90.00, 107.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA-directed RNA polymerase beta' chain / RNAP beta' subunit / Transcriptase beta' chain / RNA polymerase beta' subunit


Mass: 34489.102 Da / Num. of mol.: 1 / Fragment: residues 151-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: rpoC / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9KWU6, DNA-directed RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium cacodylate/magnesium acetate/polyethylene glycol 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92511 Å
DetectorDetector: CCD / Date: Aug 25, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92511 Å / Relative weight: 1
ReflectionResolution: 2.7→35 Å / Num. obs: 10739

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: combination of molecular replacement, SAD
Resolution: 2.7→35 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.279 560 random
Rwork0.236 --
obs0.236 10715 -
all-11794 -
Refinement stepCycle: LAST / Resolution: 2.7→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 0 0 2329

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