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- PDB-6tru: Crystal structure of the N-terminal half of the TFIIH subunit p52 -

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Basic information

Entry
Database: PDB / ID: 6tru
TitleCrystal structure of the N-terminal half of the TFIIH subunit p52
ComponentsRNA polymerase II transcription factor B subunit 2
KeywordsTRANSCRIPTION / TFIIH / DNA repair
Function / homologyTranscription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / transcription factor TFIIH core complex / ATPase activator activity / nucleotide-excision repair / RNA polymerase II transcription factor B subunit 2
Function and homology information
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKoelmel, W. / Kuper, J. / Schoenwetter, E. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KI-562/11-1 Germany
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: How to limit the speed of a motor: the intricate regulation of the XPB ATPase and translocase in TFIIH.
Authors: Kappenberger, J. / Koelmel, W. / Schoenwetter, E. / Scheuer, T. / Woerner, J. / Kuper, J. / Kisker, C.
History
DepositionDec 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 23, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 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

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Assembly

Deposited unit
B: RNA polymerase II transcription factor B subunit 2
A: RNA polymerase II transcription factor B subunit 2
C: RNA polymerase II transcription factor B subunit 2
D: RNA polymerase II transcription factor B subunit 2


Theoretical massNumber of molelcules
Total (without water)153,9404
Polymers153,9404
Non-polymers00
Water0
1
B: RNA polymerase II transcription factor B subunit 2


Theoretical massNumber of molelcules
Total (without water)38,4851
Polymers38,4851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RNA polymerase II transcription factor B subunit 2


Theoretical massNumber of molelcules
Total (without water)38,4851
Polymers38,4851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA polymerase II transcription factor B subunit 2


Theoretical massNumber of molelcules
Total (without water)38,4851
Polymers38,4851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA polymerase II transcription factor B subunit 2


Theoretical massNumber of molelcules
Total (without water)38,4851
Polymers38,4851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.309, 104.309, 164.951
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13A
23C
14B
24D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A10 - 298
2112C10 - 298
1122B10 - 298
2122D10 - 298
1132A307 - 319
2132C307 - 319
1142B307 - 319
2142D307 - 319

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.522804, -0.852124, -0.023673), (-0.850071, 0.523216, -0.060206), (0.063689, -0.011352, -0.997905)206.804016, 120.534302, -25.466841
3given(1), (1), (1)
4given(-0.481045, -0.876426, 0.021781), (-0.87582, 0.479305, -0.056627), (0.03919, -0.046316, -0.998158)201.192032, 125.141167, -21.40999
5given(1), (1), (1)
6given(-0.536201, -0.843679, -0.026361), (-0.841953, 0.536803, -0.054375), (0.060026, -0.006961, -0.998173)208.342865, 119.053932, -25.03039
7given(1), (1), (1)
8given(-0.524754, -0.85084, 0.026538), (-0.851209, 0.524149, -0.026661), (0.008774, -0.03658, -0.999292)206.108475, 121.953819, -18.13051

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Components

#1: Protein
RNA polymerase II transcription factor B subunit 2


Mass: 38485.109 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0044720 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S965

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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: 3.37 Å3/Da / Density % sol: 63.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7.5 / Details: calcium acetate, PEG 8000, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97973 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97973 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.55
11-h,-k,l20.071
11K, H, -L30.249
11-K, -H, -L40.13
ReflectionResolution: 2.8→46.97 Å / Num. obs: 49518 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.053 / Net I/σ(I): 10.7
Reflection shellResolution: 2.8→2.89 Å / Redundancy: 10.8 % / Rmerge(I) obs: 2.829 / Mean I/σ(I) obs: 1 / Num. unique obs: 4628 / CC1/2: 0.325 / Rpim(I) all: 0.901 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
Aimlessdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→46.97 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.683 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.054
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 2487 5 %RANDOM
Rwork0.1864 ---
obs0.1875 46992 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 207.69 Å2 / Biso mean: 88.934 Å2 / Biso min: 5.89 Å2
Baniso -1Baniso -2Baniso -3
1--40.27 Å2-0 Å2-0 Å2
2---40.27 Å2-0 Å2
3---80.55 Å2
Refinement stepCycle: final / Resolution: 2.8→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8566 0 0 0 8566
Num. residues----1082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138760
X-RAY DIFFRACTIONr_bond_other_d0.0040.0178476
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.64411903
X-RAY DIFFRACTIONr_angle_other_deg1.161.5719572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81651066
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.74920.7443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.002151486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8521574
X-RAY DIFFRACTIONr_chiral_restr0.0530.21149
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029566
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021880
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2364MEDIUM POSITIONAL0.070.5
1A1424TIGHT THERMAL11.20.5
1A2364MEDIUM THERMAL11.912
2B2402MEDIUM POSITIONAL0.040.5
2B1435TIGHT THERMAL17.150.5
2B2402MEDIUM THERMAL17.842
3A117MEDIUM POSITIONAL0.030.5
3A71TIGHT THERMAL8.370.5
3A117MEDIUM THERMAL10.082
4B117MEDIUM POSITIONAL0.030.5
4B71TIGHT THERMAL16.210.5
4B117MEDIUM THERMAL15.672
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 172 -
Rwork0.261 3571 -
all-3743 -
obs--99.95 %

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