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- PDB-7xgw: Apo structure of LW domain from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 7xgw
TitleApo structure of LW domain from Trypanosoma brucei
ComponentsTranscription elongation factor s-II
KeywordsTRANSCRIPTION / Transcription elongation / TFIIS / Leo1
Function / homology
Function and homology information


nucleoplasm / nucleus
Similarity search - Function
TFIIS helical bundle-like domain / Transcription factor IIS, N-terminal / TFIIS N-terminal domain profile. / TFIIS/LEDGF domain superfamily / PWWP domain / PWWP domain profile. / PWWP domain
Similarity search - Domain/homology
PWWP domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLiao, S. / Gao, J. / Chen, M. / Tu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071220 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
DepositionApr 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 24, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Transcription elongation factor s-II
A: Transcription elongation factor s-II
B: Transcription elongation factor s-II
C: Transcription elongation factor s-II
D: Transcription elongation factor s-II
E: Transcription elongation factor s-II


Theoretical massNumber of molelcules
Total (without water)89,0756
Polymers89,0756
Non-polymers00
Water1,40578
1
F: Transcription elongation factor s-II


Theoretical massNumber of molelcules
Total (without water)14,8461
Polymers14,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transcription elongation factor s-II


Theoretical massNumber of molelcules
Total (without water)14,8461
Polymers14,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Transcription elongation factor s-II


Theoretical massNumber of molelcules
Total (without water)14,8461
Polymers14,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Transcription elongation factor s-II


Theoretical massNumber of molelcules
Total (without water)14,8461
Polymers14,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Transcription elongation factor s-II


Theoretical massNumber of molelcules
Total (without water)14,8461
Polymers14,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
E: Transcription elongation factor s-II


Theoretical massNumber of molelcules
Total (without water)14,8461
Polymers14,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.724, 111.724, 93.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 254 through 265 or (resid 266...
21(chain B and (resid 254 through 272 or (resid 273...
31(chain C and (resid 254 through 265 or (resid 266...
41(chain D and (resid 254 through 264 or (resid 265...
51(chain E and (resid 254 through 265 or (resid 266...
61(chain F and (resid 254 through 264 or (resid 265...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLYSLYS(chain A and (resid 254 through 265 or (resid 266...AB254 - 26528 - 39
12GLUGLUGLUGLU(chain A and (resid 254 through 265 or (resid 266...AB26640
13ASPASPALAALA(chain A and (resid 254 through 265 or (resid 266...AB254 - 35628 - 130
14ASPASPALAALA(chain A and (resid 254 through 265 or (resid 266...AB254 - 35628 - 130
15ASPASPALAALA(chain A and (resid 254 through 265 or (resid 266...AB254 - 35628 - 130
16ASPASPALAALA(chain A and (resid 254 through 265 or (resid 266...AB254 - 35628 - 130
21ASPASPMETMET(chain B and (resid 254 through 272 or (resid 273...BC254 - 27228 - 46
22GLUGLUGLUGLU(chain B and (resid 254 through 272 or (resid 273...BC27347
23ASPASPLEULEU(chain B and (resid 254 through 272 or (resid 273...BC254 - 35228 - 126
24ASPASPLEULEU(chain B and (resid 254 through 272 or (resid 273...BC254 - 35228 - 126
25ASPASPLEULEU(chain B and (resid 254 through 272 or (resid 273...BC254 - 35228 - 126
26ASPASPLEULEU(chain B and (resid 254 through 272 or (resid 273...BC254 - 35228 - 126
31ASPASPLYSLYS(chain C and (resid 254 through 265 or (resid 266...CD254 - 26528 - 39
32GLUGLUGLUGLU(chain C and (resid 254 through 265 or (resid 266...CD26640
41ASPASPGLYGLY(chain D and (resid 254 through 264 or (resid 265...DE254 - 26428 - 38
42LYSLYSGLUGLU(chain D and (resid 254 through 264 or (resid 265...DE265 - 26639 - 40
43ASPASPLEULEU(chain D and (resid 254 through 264 or (resid 265...DE254 - 35228 - 126
44ASPASPLEULEU(chain D and (resid 254 through 264 or (resid 265...DE254 - 35228 - 126
45ASPASPLEULEU(chain D and (resid 254 through 264 or (resid 265...DE254 - 35228 - 126
46ASPASPLEULEU(chain D and (resid 254 through 264 or (resid 265...DE254 - 35228 - 126
51ASPASPLYSLYS(chain E and (resid 254 through 265 or (resid 266...EF254 - 26528 - 39
52GLUGLUGLUGLU(chain E and (resid 254 through 265 or (resid 266...EF26640
53ASPASPALAALA(chain E and (resid 254 through 265 or (resid 266...EF254 - 35328 - 127
54ASPASPALAALA(chain E and (resid 254 through 265 or (resid 266...EF254 - 35328 - 127
55ASPASPALAALA(chain E and (resid 254 through 265 or (resid 266...EF254 - 35328 - 127
56ASPASPALAALA(chain E and (resid 254 through 265 or (resid 266...EF254 - 35328 - 127
61ASPASPGLYGLY(chain F and (resid 254 through 264 or (resid 265...FA254 - 26428 - 38
62LYSLYSGLUGLU(chain F and (resid 254 through 264 or (resid 265...FA265 - 26639 - 40
63ASPASPALAALA(chain F and (resid 254 through 264 or (resid 265...FA254 - 35628 - 130
64ASPASPALAALA(chain F and (resid 254 through 264 or (resid 265...FA254 - 35628 - 130
65ASPASPALAALA(chain F and (resid 254 through 264 or (resid 265...FA254 - 35628 - 130
66ASPASPALAALA(chain F and (resid 254 through 264 or (resid 265...FA254 - 35628 - 130

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Components

#1: Protein
Transcription elongation factor s-II


Mass: 14845.907 Da / Num. of mol.: 6 / Fragment: LW domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q586Y0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 1.9 Å3/Da / Density % sol: 35.29 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 1.5M Lithium sulfate monohydrate, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.22
ReflectionResolution: 2.25→48.38 Å / Num. obs: 32354 / % possible obs: 99.4 % / Redundancy: 19.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Net I/σ(I): 19.5
Reflection shellResolution: 2.25→2.32 Å / Rmerge(I) obs: 1.111 / Num. unique obs: 2857 / CC1/2: 0.798

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FAX

7fax


Resolution: 2.25→42.265 Å / Cross valid method: THROUGHOUT / σ(F): 64.86 / Phase error: 30.58 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2299 1994 6.17 %
Rwork0.1993 30297 -
obs0.2025 32323 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.47 Å2 / Biso mean: 54.7945 Å2 / Biso min: 28.53 Å2
Refinement stepCycle: final / Resolution: 2.25→42.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4441 0 0 78 4519
Biso mean---46.44 -
Num. residues----599
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1686X-RAY DIFFRACTION10.994TORSIONAL
12B1686X-RAY DIFFRACTION10.994TORSIONAL
13C1686X-RAY DIFFRACTION10.994TORSIONAL
14D1686X-RAY DIFFRACTION10.994TORSIONAL
15E1686X-RAY DIFFRACTION10.994TORSIONAL
16F1686X-RAY DIFFRACTION10.994TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2527-2.3090.29441430.2782121226493
2.309-2.37140.28031390.26982136227594
2.3714-2.44110.2991440.26712148229294
2.4411-2.51990.29311430.25782164230794
2.5199-2.60990.25781420.25692146228894
2.6099-2.71430.28271400.24132136227694
2.7143-2.83780.24281420.22812162230494
2.8378-2.98730.27411400.22582160230094
2.9873-3.17430.28991430.23682176231994
3.1743-3.4190.25431460.21542161230794
3.419-3.76260.22251440.19082167231194
3.7626-4.30570.19211330.16482118225190
4.3057-5.41980.17171450.15652197234294
5.4198-30.5080.20651480.1812305245394
Refinement TLS params.Method: refined / Origin x: 33.5225 Å / Origin y: 0.6102 Å / Origin z: -11.2606 Å
111213212223313233
T0.4239 Å20.0381 Å2-0.0233 Å2-0.3763 Å2-0.0334 Å2--0.2803 Å2
L0.0053 °20.0402 °2-0.0134 °2-0.1478 °2-0.0593 °2--0.0109 °2
S0.0037 Å °-0.0236 Å °0.0111 Å °-0.0336 Å °0.0094 Å °0.0053 Å °-0.0064 Å °-0.0307 Å °-0.0191 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allF254 - 356
2X-RAY DIFFRACTION1allA254 - 356
3X-RAY DIFFRACTION1allB254 - 352
4X-RAY DIFFRACTION1allC254 - 353
5X-RAY DIFFRACTION1allD254 - 352
6X-RAY DIFFRACTION1allE254 - 353
7X-RAY DIFFRACTION1allS1 - 135

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