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- PDB-1l9u: THERMUS AQUATICUS RNA POLYMERASE HOLOENZYME AT 4 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1l9u
TitleTHERMUS AQUATICUS RNA POLYMERASE HOLOENZYME AT 4 A RESOLUTION
Components
  • (RNA POLYMERASE, ...) x 4
  • SIGMA FACTOR SIGA
KeywordsTRANSCRIPTION / helix-turn-helix / coiled-coil
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / : / : / : ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / protein dimerization activity / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
: / DNA-directed RNA polymerase subunit beta', hybrid domain / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. ...: / DNA-directed RNA polymerase subunit beta', hybrid domain / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / 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 / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / 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 / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit omega / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4 Å
AuthorsMurakami, K.S. / Masuda, S. / Darst, S.A.
CitationJournal: Science / Year: 2002
Title: Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution.
Authors: Murakami, K.S. / Masuda, S. / Darst, S.A.
History
DepositionMar 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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_site
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_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
A: RNA POLYMERASE, ALPHA SUBUNIT
B: RNA POLYMERASE, ALPHA SUBUNIT
C: RNA POLYMERASE, BETA SUBUNIT
D: RNA POLYMERASE, BETA-PRIME SUBUNIT
E: RNA POLYMERASE, OMEGA SUBUNIT
H: SIGMA FACTOR SIGA
J: RNA POLYMERASE, ALPHA SUBUNIT
K: RNA POLYMERASE, ALPHA SUBUNIT
L: RNA POLYMERASE, BETA SUBUNIT
M: RNA POLYMERASE, BETA-PRIME SUBUNIT
N: RNA POLYMERASE, OMEGA SUBUNIT
Q: SIGMA FACTOR SIGA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)831,26918
Polymers830,95912
Non-polymers3106
Water00
1
A: RNA POLYMERASE, ALPHA SUBUNIT
B: RNA POLYMERASE, ALPHA SUBUNIT
C: RNA POLYMERASE, BETA SUBUNIT
D: RNA POLYMERASE, BETA-PRIME SUBUNIT
E: RNA POLYMERASE, OMEGA SUBUNIT
H: SIGMA FACTOR SIGA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)415,6349
Polymers415,4796
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
J: RNA POLYMERASE, ALPHA SUBUNIT
K: RNA POLYMERASE, ALPHA SUBUNIT
L: RNA POLYMERASE, BETA SUBUNIT
M: RNA POLYMERASE, BETA-PRIME SUBUNIT
N: RNA POLYMERASE, OMEGA SUBUNIT
Q: SIGMA FACTOR SIGA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)415,6349
Polymers415,4796
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155, 271.2, 155.3
Angle α, β, γ (deg.)90, 91.4, 90
Int Tables number4
Space group name H-MP1211

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Components

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RNA POLYMERASE, ... , 4 types, 10 molecules ABJKCLDMEN

#1: Protein
RNA POLYMERASE, ALPHA SUBUNIT


Mass: 34830.895 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU8, DNA-directed RNA polymerase
#2: Protein RNA POLYMERASE, BETA SUBUNIT


Mass: 124800.898 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU7, DNA-directed RNA polymerase
#3: Protein RNA POLYMERASE, BETA-PRIME SUBUNIT


Mass: 171187.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU6, DNA-directed RNA polymerase
#4: Protein RNA POLYMERASE, OMEGA SUBUNIT


Mass: 11642.423 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9EVV4, DNA-directed RNA polymerase

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Protein , 1 types, 2 molecules HQ

#5: Protein SIGMA FACTOR SIGA


Mass: 38186.723 Da / Num. of mol.: 2 / Fragment: RESIDUES 92-438
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: RPOD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9EZJ8

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Non-polymers , 2 types, 6 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 3.92 Å3/Da / Density % sol: 68.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: HEPES, sodium formate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
20.1 MHEPES-NaOH1droppH8.0
33 Msodium formate1drop
42.4-2.6 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 6, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. all: 107237 / Num. obs: 85682 / % possible obs: 79.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 5.4
Reflection shellResolution: 4→4.14 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.357 / % possible all: 70.1
Reflection
*PLUS
Highest resolution: 4 Å / Lowest resolution: 50 Å / Num. measured all: 107237 / Rmerge(I) obs: 0.158
Reflection shell
*PLUS
% possible obs: 70.1 % / Rmerge(I) obs: 0.357

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Processing

Software
NameClassification
MLPHAREphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementHighest resolution: 4 Å / Details: the coordinates contain only a CA trace.
Refinement stepCycle: LAST / Highest resolution: 4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9375 0 0 0 9375
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor obs: 0.345 / Rfactor Rfree: 0.397 / Rfactor Rwork: 0.345
Solvent computation
*PLUS
Displacement parameters
*PLUS

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