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- PDB-3h4c: Structure of the C-terminal Domain of Transcription Factor IIB fr... -

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Basic information

Entry
Database: PDB / ID: 3h4c
TitleStructure of the C-terminal Domain of Transcription Factor IIB from Trypanosoma brucei
ComponentsTranscription factor TFIIB-like
KeywordsTRANSCRIPTION / cyclin / Transcription Factor TFIIB repeat
Function / homology
Function and homology information


transcription preinitiation complex assembly / transcription factor TFIIIB complex / RNA polymerase III type 3 promoter sequence-specific DNA binding / RNA polymerase III general transcription initiation factor activity / transcription preinitiation complex / RNA polymerase II general transcription initiation factor activity / RNA polymerase II complex binding / transcription initiation at RNA polymerase II promoter / zinc ion binding / nucleus
Similarity search - Function
Cyclin A; domain 1 - #110 / Transcription factor IIB, C-terminal module 1 / : / Transcription factor IIB C-terminal module 1 / Transcription factor IIB C-terminal module 2 / Transcription factor IIB, zinc ribbon, Trypanosome / Cyclin-like / Transcription factor TFIIB / Cyclin A; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription initiation factor IIB
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSyed Ibrahim, B. / Kanneganti, N. / Rieckhof, G.E. / Das, A. / Laurents, D.V. / Palenchar, J.B. / Bellofatto, V. / Wah, D.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of the C-terminal domain of transcription factor IIB from Trypanosoma brucei.
Authors: Ibrahim, B.S. / Kanneganti, N. / Rieckhof, G.E. / Das, A. / Laurents, D.V. / Palenchar, J.B. / Bellofatto, V. / Wah, D.A.
History
DepositionApr 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 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: Transcription factor TFIIB-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6712
Polymers28,6091
Non-polymers621
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.233, 109.233, 51.123
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-16-

HOH

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Components

#1: Protein Transcription factor TFIIB-like


Mass: 28609.207 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 427 / Gene: TFIIB-like / Production host: Escherichia coli (E. coli) / References: UniProt: Q257B3
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 24% PEG 3350, 0.2M sodium chloride, 0.1M Bis-tris (2-Bis(2-hydroxyethyl)amino-2-(hydroxymethyl)-1,3-propanediol), pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.5418
SYNCHROTRONNSLS X29A20.9791,0.9793,0.9700
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATEJun 10, 2008VariMax
ADSC QUANTUM 315r2CCDAug 11, 2008mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1VariMax opticSINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97911
30.97931
40.971
ReflectionResolution: 2.3→50 Å / Num. all: 13573 / Num. obs: 13573 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / % possible all: 94.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.5.0036refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→7.99 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.904 / SU B: 13.455 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24938 1342 10.2 %RANDOM
Rwork0.2037 ---
all0.20831 13203 --
obs0.20831 11861 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1609 0 4 56 1669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221640
X-RAY DIFFRACTIONr_angle_refined_deg1.0651.9922218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8065207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.40222.46469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03115300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2821519
X-RAY DIFFRACTIONr_chiral_restr0.0630.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211197
X-RAY DIFFRACTIONr_mcbond_it0.2991.51037
X-RAY DIFFRACTIONr_mcangle_it0.5921664
X-RAY DIFFRACTIONr_scbond_it1.1153603
X-RAY DIFFRACTIONr_scangle_it1.8954.5554
LS refinement shellResolution: 2.3→2.355 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 103 -
Rwork0.24 794 -
obs--93.93 %
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)
13.6272-6.24540.542314.9919-2.72330.8443-0.09440.0158-0.4109-0.36020.16030.80320.2256-0.082-0.06590.2493-0.0571-0.03490.09760.01330.232920.1327.89713.59
23.0197-1.24750.83893.3713-2.03533.70910.1830.3667-0.203-0.4353-0.05150.2360.3813-0.1686-0.13150.2153-0.0187-0.06260.0698-0.00360.143425.55914.0018.206
36.1309-5.43170.146111.71911.10711.2871-0.2934-0.4687-0.01790.59280.36-0.42120.19620.1967-0.06670.3027-0.0094-0.04310.11730.07210.183129.0834.47323.3
41.49750.7262-1.17742.1524-0.74632.77490.13470.02820.0344-0.1470.10860.1340.1879-0.0764-0.24320.1988-0.0019-0.03780.110.01480.178227.49521.43113.261
56.5699-5.23312.95098.8014-5.38367.0618-0.6294-0.5197-0.25510.67340.66190.4889-0.2815-0.2226-0.03260.23130.0336-0.01810.07760.02810.170926.76818.46121.365
63.7005-0.15213.109512.5445-3.95837.5558-0.0216-0.347-0.08860.1674-0.3041-1.1910.03540.69920.32570.09620.04310.00430.2660.01380.271441.16415.89915.731
78.2742-4.56213.18017.2018-2.85358.54010.0239-0.0357-0.21580.13360.0980.0293-0.4302-0.0386-0.12180.2258-0.01910.04990.0939-0.00630.148531.37833.2836.722
81.5970.71850.79371.99551.699410.7938-0.1596-0.0087-0.0006-0.08180.2368-0.3619-0.39640.5207-0.07730.1904-0.00410.01460.0767-0.02980.130136.34641.32913.699
96.0378-0.96670.638713.3838-3.1253.18820.0028-0.1080.3445-0.32420.00720.221-0.0452-0.1721-0.010.1978-0.0050.00080.0755-0.02980.139428.70741.8712.941
107.98814.46980.563110.17740.58262.6606-0.1310.15990.8021-0.0820.31690.6237-1.1117-0.2709-0.18590.550.08070.0040.08370.07360.211724.38145.96710.338
116.07163.24961.02817.50561.21722.64770.0577-0.11950.16460.31710.0597-0.0407-0.2979-0.1911-0.11740.25880.0567-0.0150.0444-0.00960.05827.30943.57318.416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A94 - 105
2X-RAY DIFFRACTION2A106 - 129
3X-RAY DIFFRACTION3A130 - 142
4X-RAY DIFFRACTION4A143 - 168
5X-RAY DIFFRACTION5A169 - 183
6X-RAY DIFFRACTION6A184 - 196
7X-RAY DIFFRACTION7A197 - 215
8X-RAY DIFFRACTION8A216 - 241
9X-RAY DIFFRACTION9A242 - 255
10X-RAY DIFFRACTION10A256 - 285
11X-RAY DIFFRACTION11A286 - 313

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