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- PDB-5obz: low resolution structure of the p34ct/p44ct minimal complex -

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Basic information

Entry
Database: PDB / ID: 5obz
Titlelow resolution structure of the p34ct/p44ct minimal complex
Components(Putative transcription factor) x 2
KeywordsTRANSCRIPTION / complex
Function / homology
Function and homology information


transcription factor TFIIH holo complex / transcription factor TFIIH core complex / nucleotide-excision repair / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / zinc ion binding / metal ion binding
Similarity search - Function
TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / von Willebrand factor, type A domain / C1-like domain superfamily ...TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / von Willebrand factor, type A domain / C1-like domain superfamily / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / von Willebrand factor A-like domain superfamily / Zinc finger C2H2-type / Zinc finger, RING/FYVE/PHD-type / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
General transcription and DNA repair factor IIH subunit TFB4 / General transcription and DNA repair factor IIH
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsSchoenwetter, E. / Koelmel, W. / Schmitt, D.R. / Kuper, J. / Kisker, C.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Excellence Initiative to the Graduate School of Life SCiences, University of Wuerzburg Germany
German Research FoundationKI-562/7-1 Germany
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: The intricate network between the p34 and p44 subunits is central to the activity of the transcription/DNA repair factor TFIIH.
Authors: Radu, L. / Schoenwetter, E. / Braun, C. / Marcoux, J. / Koelmel, W. / Schmitt, D.R. / Kuper, J. / Cianferani, S. / Egly, J.M. / Poterszman, A. / Kisker, C.
History
DepositionJun 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative transcription factor
B: Putative transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9544
Polymers49,8232
Non-polymers1312
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-21 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.212, 138.212, 95.235
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Putative transcription factor /


Mass: 31972.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0004460 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: G0RXV8
#2: Protein Putative transcription factor /


Mass: 17850.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0002690 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: G0RZE6
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.27 Å3/Da / Density % sol: 62.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 20,000 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.7→45.2 Å / Num. obs: 6120 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 9.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NUS

5nus


Resolution: 3.7→45.2 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 39.081 / SU ML: 0.506 / Cross valid method: THROUGHOUT / ESU R Free: 0.553 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24623 278 4.6 %RANDOM
Rwork0.19616 ---
obs0.19843 5828 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 152.72 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å21.25 Å20 Å2
2--2.5 Å2-0 Å2
3----8.12 Å2
Refinement stepCycle: 1 / Resolution: 3.7→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 2 1 2082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192133
X-RAY DIFFRACTIONr_bond_other_d0.0030.022002
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9552901
X-RAY DIFFRACTIONr_angle_other_deg1.1073.0034619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6125269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13323.25383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.33915331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.081513
X-RAY DIFFRACTIONr_chiral_restr0.1090.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212343
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02430
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_it10.35215.3591091
X-RAY DIFFRACTIONr_mcbond_other10.33815.3581090
X-RAY DIFFRACTIONr_mcangle_it16.15722.9941355
X-RAY DIFFRACTIONr_mcangle_other16.15622.9971356
X-RAY DIFFRACTIONr_scbond_it9.75515.9321042
X-RAY DIFFRACTIONr_scbond_other9.75115.9351043
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.26823.6771547
X-RAY DIFFRACTIONr_long_range_B_refined20.9264767
X-RAY DIFFRACTIONr_long_range_B_other20.9254768
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.7→3.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 16 -
Rwork0.367 421 -
obs--99.54 %

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