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- PDB-2pa8: X-Ray Crystal Structure of the D/L Subcomplex of the Sulfolobus S... -

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Basic information

Entry
Database: PDB / ID: 2pa8
TitleX-Ray Crystal Structure of the D/L Subcomplex of the Sulfolobus Solfataricus RNA polymerase
Components
  • DNA-directed RNA polymerase subunit DPolymerase
  • DNA-directed RNA polymerase subunit LPolymerase
KeywordsTRANSFERASE / Ferredoxin-like Fe-S binding motif / Platform for RNA polymerase assembly
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / DNA binding / metal ion binding / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #20 / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Gyrase A; domain 2 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerases L / 13 to 16 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 ...Alpha-Beta Plaits - #20 / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Gyrase A; domain 2 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerases L / 13 to 16 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / Beta Complex / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo11
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsHirata, A. / Murakami, K.S.
CitationJournal: Nature / Year: 2008
Title: The X-ray crystal structure of RNA polymerase from Archaea.
Authors: Hirata, A. / Klein, B.J. / Murakami, K.S.
History
DepositionMar 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA-directed RNA polymerase subunit D
L: DNA-directed RNA polymerase subunit L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0214
Polymers40,6292
Non-polymers3922
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.703, 93.346, 128.277
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11D-3237-

HOH

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Components

#1: Protein DNA-directed RNA polymerase subunit D / Polymerase


Mass: 30330.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: rpoD / Plasmid: pET21-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus / References: UniProt: P95989, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit L / Polymerase


Mass: 10298.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: rpoL / Plasmid: pET21-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus / References: UniProt: Q980K0, DNA-directed RNA polymerase
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.57 Å3/Da / Density % sol: 52.08 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Sodium citrate, 22 %(saturation) ammonium sulfate, 12 % (w/v) PEG 4000, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 11, 2006 / Details: Pt-coated mirror
RadiationMonochromator: Si-111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 85672 / % possible obs: 98 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.087 / Χ2: 1.001 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.765.80.8843710.838196.5
1.76-1.836.90.65443670.87197.1
1.83-1.917.40.43843970.926197.4
1.91-2.027.50.29544170.965197.7
2.02-2.147.50.19544491.004197.9
2.14-2.317.40.14644591.147198.3
2.31-2.547.40.10445051.043198.5
2.54-2.917.30.07545131.062198.7
2.91-3.667.20.05445691.255199.2
3.66-5070.04647110.844198.3

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.539 / Packing: 0.544
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Rotation4 Å15 Åfast direct99.3 0
Translation4 Å15 Ågeneral99.3 0

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
RESOLVE2.06phasing
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R9T

1r9t


Resolution: 1.76→15 Å / σ(F): 0 / Details: THE FRIEDEL PAIRS WERE USED FOR phasing
RfactorNum. reflection% reflection
Rfree0.247 7258 9.1 %
Rwork0.21 --
obs-73903 92.3 %
Solvent computationBsol: 45.173 Å2
Displacement parametersBiso mean: 23.787 Å2
Baniso -1Baniso -2Baniso -3
1-2.494 Å20 Å20 Å2
2---6.067 Å20 Å2
3---3.573 Å2
Refinement stepCycle: LAST / Resolution: 1.76→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2837 0 12 288 3137
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2551.5
X-RAY DIFFRACTIONc_scbond_it2.4652
X-RAY DIFFRACTIONc_mcangle_it1.8492
X-RAY DIFFRACTIONc_scangle_it3.6822.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.76-1.820.3096240.298X-RAY DIFFRACTION577872
1.82-1.90.3037100.269X-RAY DIFFRACTION587374
1.9-1.980.2726900.241X-RAY DIFFRACTION641380
1.98-2.090.2616590.214X-RAY DIFFRACTION670484
2.09-2.220.2537220.206X-RAY DIFFRACTION680285
2.22-2.390.2497360.21X-RAY DIFFRACTION685586
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2iron_sulphur.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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