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- PDB-3lti: Crystal structure of the Escherichia coli RNA polymerase beta sub... -

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Basic information

Entry
Database: PDB / ID: 3lti
TitleCrystal structure of the Escherichia coli RNA polymerase beta subunit beta2-betai4 domains
ComponentsDNA-directed RNA polymerase subunit beta
KeywordsTRANSFERASE / BBM2 / DNA-directed RNA polymerase / Nucleotidyltransferase / Transcription
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 / DNA-templated transcription initiation ...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 / DNA-templated transcription initiation / transcription antitermination / cell motility / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / intracellular iron ion homeostasis / response to antibiotic / DNA binding / membrane / cytosol / cytoplasm
Similarity search - Function
Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 ...Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsDarst, S.A. / Opalka, N.
CitationJournal: PLoS Biol / Year: 2010
Title: Complete structural model of Escherichia coli RNA polymerase from a hybrid approach.
Authors: Natacha Opalka / Jesse Brown / William J Lane / Kelly-Anne F Twist / Robert Landick / Francisco J Asturias / Seth A Darst /
Abstract: The Escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. Nevertheless, a molecular understanding of the ...The Escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. Nevertheless, a molecular understanding of the details of E. coli transcription and its regulation, and therefore its full exploitation as a model system, has been hampered by the absence of high-resolution structural information on E. coli RNA polymerase (RNAP). We use a combination of approaches, including high-resolution X-ray crystallography, ab initio structural prediction, homology modeling, and single-particle cryo-electron microscopy, to generate complete atomic models of E. coli core RNAP and an E. coli RNAP ternary elongation complex. The detailed and comprehensive structural descriptions can be used to help interpret previous biochemical and genetic data in a new light and provide a structural framework for designing experiments to understand the function of the E. coli lineage-specific insertions and their role in the E. coli transcription program.
History
DepositionFeb 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Nov 23, 2011Group: Database references
Revision 1.4Feb 22, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit beta


Theoretical massNumber of molelcules
Total (without water)34,6371
Polymers34,6371
Non-polymers00
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.314, 52.039, 61.826
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly comprises the asymmetric unit

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Components

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


Mass: 34636.602 Da / Num. of mol.: 1 / Fragment: beta2-beta-i-4 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12
Gene: b3987, groN, JW3950, nitB, rif, ron, rpoB, stl, stv, tabD
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A8V2, DNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M potassium-sodium tartrate, 20% PEG 3350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X3A / Wavelength: 0.9919 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. obs: 42737 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rsym value: 0.069 / Net I/σ(I): 40
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.416 / % possible all: 94

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
REFMAC5.5.0091refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→14.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 2.653 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.094
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22955 1398 3.2 %RANDOM
Rwork0.20791 ---
obs0.20884 42737 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.586 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2---0.55 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.6→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 0 378 2695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222397
X-RAY DIFFRACTIONr_bond_other_d0.0020.021685
X-RAY DIFFRACTIONr_angle_refined_deg1.1342.013243
X-RAY DIFFRACTIONr_angle_other_deg0.81234095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0595296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.54923.852122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37315411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4231524
X-RAY DIFFRACTIONr_chiral_restr0.0620.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212636
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02491
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5141.51435
X-RAY DIFFRACTIONr_mcbond_other0.0831.5578
X-RAY DIFFRACTIONr_mcangle_it0.98322331
X-RAY DIFFRACTIONr_scbond_it1.4353962
X-RAY DIFFRACTIONr_scangle_it2.4564.5905
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.249 3118 -
Rfree-0 -
obs--100 %

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