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- PDB-7fax: Complex structure of TbLeo1 and LW domain from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 7fax
TitleComplex structure of TbLeo1 and LW domain from Trypanosoma brucei
Components
  • TbLW
  • TbLeo1 peptide
KeywordsTRANSCRIPTION / LW / Paf1C
Function / homology
Function and homology information


RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Leo1-like protein / Leo1-like protein / TFIIS N-terminal domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / TFIIS/LEDGF domain superfamily / PWWP domain / PWWP domain profile. / PWWP domain
Similarity search - Domain/homology
RNA polymerase-associated protein LEO1 / PWWP domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsLiao, S. / Gao, J. / Tu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31500601 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Structural basis for evolutionarily conserved interactions between TFIIS and Paf1C.
Authors: Gao, J. / Jishage, M. / Wang, Y. / Wang, R. / Chen, M. / Zhu, Z. / Zhang, J. / Diwu, Y. / Xu, C. / Liao, S. / Roeder, R.G. / Tu, X.
History
DepositionJul 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TbLW
B: TbLeo1 peptide


Theoretical massNumber of molelcules
Total (without water)14,4132
Polymers14,4132
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-12 kcal/mol
Surface area6770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.919, 79.919, 38.843
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein TbLW


Mass: 12410.729 Da / Num. of mol.: 1 / Mutation: C274M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb927.2.3480
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q586Y0
#2: Protein/peptide TbLeo1 peptide


Mass: 2002.246 Da / Num. of mol.: 1 / Mutation: F79L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb09.211.3840
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q38DC5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 3.5M NaCOOH, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.35
ReflectionResolution: 1.6→50 Å / Num. obs: 22291 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.077 / Net I/σ(I): 75.7
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1633 / CC1/2: 0.867 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→21.969 Å / Cross valid method: THROUGHOUT / σ(F): 44.36 / Phase error: 38.73 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2384 2230 10 %
Rwork0.2149 20043 -
obs0.2207 22291 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.7 Å2 / Biso mean: 13.5037 Å2 / Biso min: 3.86 Å2
Refinement stepCycle: final / Resolution: 1.8→21.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 0 23 933
Biso mean---25.68 -
Num. residues----117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8002-1.83930.24931380.24931274141290
1.8393-1.8820.24091380.23991240137890
1.882-1.9290.24111480.24591294144290
1.929-1.98110.26431360.23391221135790
1.9811-2.03940.26991380.24971240137890
2.0394-2.10510.2491400.231240138090
2.1051-2.18020.22291380.23651269140790
2.1802-2.26740.28251380.22691248138690
2.2674-2.37040.25771370.22221249138690
2.3704-2.4950.30841320.23621271140391
2.495-2.65090.26751330.22821231136490
2.6509-2.85490.24451470.21671269141690
2.8549-3.14090.27181420.22951259140190
3.1409-3.59250.24591360.22071241137790
3.5925-4.5150.1881540.17691233138789
4.515-18.3680.20581350.17771264139990
Refinement TLS params.Method: refined / Origin x: 14.1551 Å / Origin y: 11.5895 Å / Origin z: 11.9306 Å
111213212223313233
T0.0614 Å2-0.0047 Å2-0.0167 Å2-0.0393 Å20.0201 Å2--0.0691 Å2
L1.2189 °20.2847 °20.2034 °2-1.0662 °20.0038 °2--1.3143 °2
S-0.0083 Å °-0.034 Å °0.0409 Å °-0.0374 Å °-0.0155 Å °-0.0674 Å °0.0385 Å °-0.029 Å °0.0012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 109
2X-RAY DIFFRACTION1allB123 - 136
3X-RAY DIFFRACTION1allS1 - 29

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