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- PDB-8h6r: LW Domain of Arabidopsis thaliana TFIIS -

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Basic information

Entry
Database: PDB / ID: 8h6r
TitleLW Domain of Arabidopsis thaliana TFIIS
ComponentsTranscription elongation factor TFIIS
KeywordsTRANSCRIPTION / transcription factor
Function / homology
Function and homology information


seed dormancy process / negative regulation of flower development / response to gibberellin / seed germination / regulation of transcription elongation by RNA polymerase II / translation elongation factor activity / transcription elongation by RNA polymerase II / DNA-templated transcription / zinc ion binding / nucleus
Similarity search - Function
Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / TFIIS helical bundle-like domain ...Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / TFIIS helical bundle-like domain / Transcription factor IIS, N-terminal / TFIIS N-terminal domain profile. / TFIIS/LEDGF domain superfamily / Zinc finger TFIIS-type signature. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger
Similarity search - Domain/homology
Transcription elongation factor TFIIS
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: LW Domain of Arabidopsis thaliana TFIIS
Authors: Wang, Y.
History
DepositionOct 18, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription elongation factor TFIIS


Theoretical massNumber of molelcules
Total (without water)9,4111
Polymers9,4111
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.375, 65.375, 52.446
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Transcription elongation factor TFIIS / Protein REDUCED DORMANCY 2


Mass: 9410.918 Da / Num. of mol.: 1 / Fragment: LW Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TFIIS, RDO2, At2g38560
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9ZVH8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris, 0.2 M sodium trihydrate, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→12.99 Å / Num. obs: 3963 / % possible obs: 99.57 % / Redundancy: 8.2 % / Biso Wilson estimate: 36.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.121 / Net I/σ(I): 9.9
Reflection shellResolution: 2.6→2.72 Å / Num. unique obs: 3963 / CC1/2: 0.882

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: predict structure

Resolution: 2.6→12.99 Å / SU ML: 0.307 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.4968
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.27 387 9.77 %
Rwork0.2335 3576 -
obs0.2372 3963 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.92 Å2
Refinement stepCycle: LAST / Resolution: 2.6→12.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms653 0 0 27 680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048661
X-RAY DIFFRACTIONf_angle_d0.5967893
X-RAY DIFFRACTIONf_chiral_restr0.038110
X-RAY DIFFRACTIONf_plane_restr0.0035111
X-RAY DIFFRACTIONf_dihedral_angle_d3.441988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.970.28711280.30421184X-RAY DIFFRACTION98.8
2.97-3.730.33881280.25361175X-RAY DIFFRACTION100
3.73-12.990.22611310.19541217X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: -26.3831924801 Å / Origin y: 0.870330105241 Å / Origin z: 0.113210949457 Å
111213212223313233
T0.249288144585 Å2-0.030283386991 Å2-0.0395016509974 Å2-0.175875295997 Å20.0528891582684 Å2--0.214604027333 Å2
L2.74042032971 °20.227196094339 °2-0.217358143798 °2-3.57205426338 °2-0.259539046187 °2--8.15942100734 °2
S0.169350642422 Å °-0.0300618006735 Å °0.120276373382 Å °-0.275443575869 Å °-0.112301731231 Å °-0.231388157341 Å °-0.377603485115 Å °0.403636623941 Å °-0.133143309617 Å °
Refinement TLS groupSelection details: all

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