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- PDB-2auk: Structure of E. coli RNA polymerase beta' G/G' insert -

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Basic information

Entry
Database: PDB / ID: 2auk
TitleStructure of E. coli RNA polymerase beta' G/G' insert
ComponentsDNA-directed RNA polymerase beta' chain
KeywordsTRANSFERASE / sandwich-barrel hybrid motif
Function / homology
Function and homology information


submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination ...submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / intracellular iron ion homeostasis / response to antibiotic / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
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 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit ...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 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit beta'
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 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 28, 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 beta' chain
B: DNA-directed RNA polymerase beta' chain
C: DNA-directed RNA polymerase beta' chain
D: DNA-directed RNA polymerase beta' chain
E: DNA-directed RNA polymerase beta' chain


Theoretical massNumber of molelcules
Total (without water)100,6835
Polymers100,6835
Non-polymers00
Water8,233457
1
A: DNA-directed RNA polymerase beta' chain


Theoretical massNumber of molelcules
Total (without water)20,1371
Polymers20,1371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA-directed RNA polymerase beta' chain


Theoretical massNumber of molelcules
Total (without water)20,1371
Polymers20,1371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA-directed RNA polymerase beta' chain


Theoretical massNumber of molelcules
Total (without water)20,1371
Polymers20,1371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA-directed RNA polymerase beta' chain


Theoretical massNumber of molelcules
Total (without water)20,1371
Polymers20,1371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: DNA-directed RNA polymerase beta' chain


Theoretical massNumber of molelcules
Total (without water)20,1371
Polymers20,1371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
B: DNA-directed RNA polymerase beta' chain
C: DNA-directed RNA polymerase beta' chain

A: DNA-directed RNA polymerase beta' chain
D: DNA-directed RNA polymerase beta' chain
E: DNA-directed RNA polymerase beta' chain


Theoretical massNumber of molelcules
Total (without water)100,6835
Polymers100,6835
Non-polymers00
Water905
TypeNameSymmetry operationNumber
crystal symmetry operation1_454x-1,y,z-11
identity operation1_555x,y,z1
Buried area9350 Å2
ΔGint-37 kcal/mol
Surface area42860 Å2
MethodPISA
7
E: DNA-directed RNA polymerase beta' chain

A: DNA-directed RNA polymerase beta' chain
B: DNA-directed RNA polymerase beta' chain
C: DNA-directed RNA polymerase beta' chain
D: DNA-directed RNA polymerase beta' chain


Theoretical massNumber of molelcules
Total (without water)100,6835
Polymers100,6835
Non-polymers00
Water905
TypeNameSymmetry operationNumber
crystal symmetry operation1_656x+1,y,z+11
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-36 kcal/mol
Surface area43090 Å2
MethodPISA
8


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint-37 kcal/mol
Surface area42560 Å2
MethodPISA
9
E: DNA-directed RNA polymerase beta' chain

B: DNA-directed RNA polymerase beta' chain
C: DNA-directed RNA polymerase beta' chain


Theoretical massNumber of molelcules
Total (without water)60,4103
Polymers60,4103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation1_656x+1,y,z+11
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-16 kcal/mol
Surface area27080 Å2
MethodPISA
10
A: DNA-directed RNA polymerase beta' chain
D: DNA-directed RNA polymerase beta' chain


Theoretical massNumber of molelcules
Total (without water)40,2732
Polymers40,2732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-11 kcal/mol
Surface area18240 Å2
MethodPISA
11
A: DNA-directed RNA polymerase beta' chain
B: DNA-directed RNA polymerase beta' chain
C: DNA-directed RNA polymerase beta' chain
D: DNA-directed RNA polymerase beta' chain


Theoretical massNumber of molelcules
Total (without water)80,5474
Polymers80,5474
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-28 kcal/mol
Surface area34360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.030, 95.130, 86.070
Angle α, β, γ (deg.)90.00, 92.06, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthe biological assembly is one monomer of the five chains present in the asymmetric unit

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Components

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


Mass: 20136.660 Da / Num. of mol.: 5 / Fragment: residues 5-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC, tabB / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A8T7, DNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: CHES/sodium formate/dioxane, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.97156, 0.9794, 0.96384
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971561
20.97941
30.963841
ReflectionResolution: 2.19→35 Å / Num. obs: 43459

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→35 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.264 3069 random
Rwork0.225 --
obs0.225 38181 -
all-41624 -
Refinement stepCycle: LAST / Resolution: 2.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6849 0 0 457 7306

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