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- PDB-1q1h: An extended winged helix domain in general transcription factor E... -

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Basic information

Entry
Database: PDB / ID: 1q1h
TitleAn extended winged helix domain in general transcription factor E/IIE alpha
ComponentsTranscription Factor E
KeywordsTRANSCRIPTION / TFE / TFIIE / transcription initiation / preinitiation complex / RNA polymerase II / transcription bubble / promoter melting / TFIIH
Function / homology
Function and homology information


transcription open complex formation at RNA polymerase II promoter / RNA polymerase II complex binding / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcription factor TFE, archaea / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription factor E / TFIIE alpha subunit / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Transcription factor TFE, archaea / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription factor E / TFIIE alpha subunit / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription factor E
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsMeinhart, A. / Blobel, J. / Cramer, P.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: An Extended Winged Helix Domain in General Transcription Factor E/IIE alpha
Authors: Meinhart, A. / Blobel, J. / Cramer, P.
History
DepositionJul 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription Factor E


Theoretical massNumber of molelcules
Total (without water)13,0911
Polymers13,0911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.1, 66.1, 92.7
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Cell settinghexagonal
Space group name H-MP6122

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Components

#1: Protein Transcription Factor E / TFE / TFIIE alpha subunit homolog / tfE


Mass: 13091.107 Da / Num. of mol.: 1 / Fragment: residue 1-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: tfE / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q980M5

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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: 2.23 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: TRIS-Cl, sodium acetate, PEG 1000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMHEPES1droppH7.5
2200 mM1dropNaCl
31 mMEDTA1drop
410000 nM1dropZnCl2
55 mMdithiothreitol1drop
615 mg/mlprotein1drop
7100 mMTris-Cl1reservoirpH8.5
8200 mM1reservoirNaOAc
930 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 2, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 3025 / Num. obs: 3025 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 20 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 100 % / Num. unique obs: 292 / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 9.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.9→6.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.321 146 5.5 %RANDOM
Rwork0.315 ---
all0.339 2641 --
obs0.3151 2641 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.9 Å21.559 Å20 Å2
2---3.9 Å20 Å2
3---7.799 Å2
Refinement stepCycle: LAST / Resolution: 2.9→6.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms701 0 0 0 701
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.4442.5
X-RAY DIFFRACTIONc_mcangle_it33
X-RAY DIFFRACTIONc_scbond_it3.8483
X-RAY DIFFRACTIONc_scangle_it4.6563.5
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.33
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 6.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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