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- PDB-4pn7: Crystal Structure of the TFIIH p34 N-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 4pn7
TitleCrystal Structure of the TFIIH p34 N-terminal Domain
ComponentsPutative transcription factor
KeywordsTRANSCRIPTION / vWA Domain
Function / homology
Function and homology information


transcription factor TFIIH core complex / transcription factor TFIIH holo complex / nucleotide-excision repair / regulation of DNA-templated transcription / metal ion binding
Similarity search - Function
TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / von Willebrand factor, type A domain / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
General transcription and DNA repair factor IIH subunit TFB4
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.801 Å
AuthorsSchmitt, D.R. / Kuper, J. / Elias, A. / Kisker, C.
CitationJournal: Plos One / Year: 2014
Title: The Structure of the TFIIH p34 Subunit Reveals a Von Willebrand Factor A Like Fold.
Authors: Schmitt, D.R. / Kuper, J. / Elias, A. / Kisker, C.
History
DepositionMay 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative transcription factor


Theoretical massNumber of molelcules
Total (without water)31,9731
Polymers31,9731
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)257.110, 257.110, 257.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

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Components

#1: Protein Putative transcription factor / TFIIH Subunit p34


Mass: 31972.957 Da / Num. of mol.: 1 / Fragment: N-terminal Domain (UNP residues 1-277)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / Gene: CTHT_0004460 / Plasmid: pBADM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus RIL / References: UniProt: G0RXV8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.07 Å3/Da / Density % sol: 59.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Crystals grew from protein solution in 20 mM Tris-HCl pH 8.0, 150 mM KCl and 1 mM TCEP over a reservoir containing the protein buffer including 50 - 500 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.91985 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2012
RadiationMonochromator: Channel-Cut Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91985 Å / Relative weight: 1
ReflectionResolution: 2.801→148.443 Å / Num. all: 18512 / Num. obs: 18512 / % possible obs: 100 % / Redundancy: 70.5 % / Biso Wilson estimate: 94.32 Å2 / Rpim(I) all: 0.019 / Rrim(I) all: 0.155 / Rsym value: 0.153 / Net I/av σ(I): 2.159 / Net I/σ(I): 20.9 / Num. measured all: 1305233
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.8-2.9576.82.5980.320169826250.2972.5982.9100
2.95-3.1374.91.6050.418657524900.1861.6054.6100
3.13-3.3569.10.7970.916326923620.0960.7978.6100
3.35-3.6176.70.4091.716913122060.0470.40916.5100
3.61-3.9671.50.2272.814572520370.0270.22725.5100
3.96-4.4370.20.1324.613072918610.0160.13235.4100
4.43-5.1170.10.0966.411660316630.0120.09640.6100
5.11-6.2664.50.0986.19210014270.0130.09838.9100
6.26-8.8556.70.06486445311360.0090.06438.3100
8.85-77.52249.60.0644.5349507050.010.06438.199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
SCALA3.3.21data scaling
PDB_EXTRACT3.14data extraction
Cootmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.801→77.522 Å / FOM work R set: 0.8305 / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.238 956 5.17 %Free R value set from data that resulted in the model used for MR.
Rwork0.2187 17530 --
obs0.2197 18486 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 284.6 Å2 / Biso mean: 96.5 Å2 / Biso min: 61.29 Å2
Refinement stepCycle: final / Resolution: 2.801→77.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 0 0 5 1578
Biso mean---88.86 -
Num. residues----209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041601
X-RAY DIFFRACTIONf_angle_d0.7832185
X-RAY DIFFRACTIONf_chiral_restr0.03273
X-RAY DIFFRACTIONf_plane_restr0.004275
X-RAY DIFFRACTIONf_dihedral_angle_d13.028558
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8006-2.94830.28181400.262724292569
2.9483-3.1330.33331310.266524502581
3.133-3.37490.26471310.246424542585
3.3749-3.71460.23591450.229924562601
3.7146-4.2520.24211320.201325012633
4.252-5.35690.23011340.185525392673
5.3569-77.55130.22291430.23127012844
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.7199-5.72062.78784.1852-3.64116.62780.24211.42621.94180.2637-1.083-0.8225-0.62040.00880.41460.6588-0.07540.03030.82190.02491.2308-21.0794-4.710946.123
25.4518-4.14594.45976.9364-0.19426.1923-0.2779-0.4675-0.85370.46940.6355-0.12310.6741-0.9404-0.02850.8476-0.13080.08710.74130.10470.9842-14.8279-25.970559.5002
39.7275-6.34265.52984.5194-3.50817.76350.1072-0.2343-0.8880.39870.56180.45860.481-1.6489-0.47630.6137-0.13380.00730.8856-0.00320.972-25.4822-16.88149.3785
42.3871-1.72841.61548.5303-1.48175.57760.09311.11550.1924-0.3636-0.3059-0.15710.10850.10050.20190.6139-0.17250.11440.906-0.00730.8858-15.3442-13.410344.5509
54.6596-4.11754.26093.8612-2.87018.65640.3712.76930.2142-1.5012-0.866-0.15980.7198-0.78590.08930.8098-0.08750.05111.37530.01770.9064-20.3885-18.795239.9045
63.7546-1.1797-1.38532.2009-0.87168.14870.64810.16740.26390.0216-0.3624-2.02210.2694-0.2760.36660.9288-0.1141-0.05750.78040.12931.2957-4.0618-26.441153.3562
73.05331.6808-0.7684.26420.6722.4596-0.01440.4210.918-0.03670.0542-0.3057-0.1779-0.22640.00220.67-0.08210.00020.79910.15371.3592-9.3537-4.052547.4729
88.15463.6463-2.21062.6860.02747.90770.7124-0.5380.98551.9242-0.4294-1.1554-0.25370.4353-0.25660.6984-0.0759-0.06970.7552-0.15211.0844-11.3188-7.986159.7942
93.85340.8092-3.20533.21821.44524.0951.3849-1.18291.24621.402-1.0983-0.5495-0.3918-0.1862-0.33280.8954-0.23130.08990.87740.00581.0516-14.2492-3.876861.9185
103.67554.38751.48756.21673.33982.8318-0.0216-0.18710.46670.86780.14691.30570.1313-1.5841-0.42990.6475-0.14980.16821.0974-0.03180.9451-25.5983-14.227660.4571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 30 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 44 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 61 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 82 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 83 through 126 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 127 through 141 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 142 through 230 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 231 through 250 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 251 through 260 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 261 through 274 )A0

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