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- PDB-6i59: Long wavelength native-SAD phasing of Sen1 helicase -

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Basic information

Entry
Database: PDB / ID: 6i59
TitleLong wavelength native-SAD phasing of Sen1 helicase
ComponentsHelicase SEN1
KeywordsDNA BINDING PROTEIN / Sen1 helicase / Super family 1B / Long-wavelength native-SAD phasing / native-SAD / S-SAD
Function / homology
Function and homology information


transcription termination site sequence-specific DNA binding / negative regulation of flocculation / 5'-3' DNA/RNA helicase activity / Nrd1 complex / sno(s)RNA 3'-end processing / DNA-templated DNA replication maintenance of fidelity / snRNA processing / mRNA 3'-end processing / tRNA processing / termination of RNA polymerase II transcription ...transcription termination site sequence-specific DNA binding / negative regulation of flocculation / 5'-3' DNA/RNA helicase activity / Nrd1 complex / sno(s)RNA 3'-end processing / DNA-templated DNA replication maintenance of fidelity / snRNA processing / mRNA 3'-end processing / tRNA processing / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / transcription-coupled nucleotide-excision repair / cell redox homeostasis / maturation of SSU-rRNA / replication fork / small-subunit processome / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / rRNA processing / 5'-3' DNA helicase activity / nuclear body / hydrolase activity / protein domain specific binding / mRNA binding / DNA damage response / regulation of transcription by RNA polymerase II / nucleolus / RNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Helicase Sen1, 1B domain / Helicase Sen1, N-terminal / SEN1 N terminal / DNA2/NAM7 helicase, helicase domain / AAA domain / : / DNA2/NAM7-like helicase / DNA2/NAM7 helicase-like, C-terminal / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Helicase SEN1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsBasu, S. / Olieric, V. / Matsugaki, N. / Kawano, Y. / Takashi, T. / Huang, C.Y. / Leonarski, F. / Yamada, Y. / Vera, L. / Olieric, N. ...Basu, S. / Olieric, V. / Matsugaki, N. / Kawano, Y. / Takashi, T. / Huang, C.Y. / Leonarski, F. / Yamada, Y. / Vera, L. / Olieric, N. / Basquin, J. / Wojdyla, J.A. / Diederichs, K. / Yamamoto, M. / Bunk, O. / Wang, M.
Citation
Journal: Iucrj / Year: 2019
Title: Long-wavelength native-SAD phasing: opportunities and challenges.
Authors: Basu, S. / Olieric, V. / Leonarski, F. / Matsugaki, N. / Kawano, Y. / Takashi, T. / Huang, C.Y. / Yamada, Y. / Vera, L. / Olieric, N. / Basquin, J. / Wojdyla, J.A. / Bunk, O. / Diederichs, K. ...Authors: Basu, S. / Olieric, V. / Leonarski, F. / Matsugaki, N. / Kawano, Y. / Takashi, T. / Huang, C.Y. / Yamada, Y. / Vera, L. / Olieric, N. / Basquin, J. / Wojdyla, J.A. / Bunk, O. / Diederichs, K. / Yamamoto, M. / Wang, M.
#1: Journal: Iucrj / Year: 2019
Title: Long-wavelength native-SAD phasing: opportunities and challenges.
Authors: Basu, S. / Olieric, V. / Leonarski, F. / Matsugaki, N. / Kawano, Y. / Takashi, T. / Huang, C.Y. / Yamada, Y. / Vera, L. / Olieric, N. / Basquin, J. / Wojdyla, J.A. / Bunk, O. / Diederichs, K. ...Authors: Basu, S. / Olieric, V. / Leonarski, F. / Matsugaki, N. / Kawano, Y. / Takashi, T. / Huang, C.Y. / Yamada, Y. / Vera, L. / Olieric, N. / Basquin, J. / Wojdyla, J.A. / Bunk, O. / Diederichs, K. / Yamamoto, M. / Wang, M.
#2: Journal: Iucrj / Year: 2019
Title: Long-wavelength native-SAD phasing: opportunities and challenges
Authors: Basu, S. / Olieric, V. / Leonarski, F. / Matsugaki, N. / Kawano, Y. / Takashi, T. / Huang, C.Y. / Yamada, Y. / Vera, L. / Olieric, N. / Basquin, J. / Wojdyla, J.A. / Diederichs, K. / ...Authors: Basu, S. / Olieric, V. / Leonarski, F. / Matsugaki, N. / Kawano, Y. / Takashi, T. / Huang, C.Y. / Yamada, Y. / Vera, L. / Olieric, N. / Basquin, J. / Wojdyla, J.A. / Diederichs, K. / Yamamoto, M. / Bunk, O. / Wang, M.
History
DepositionNov 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author
Revision 1.2May 8, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.3May 29, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Revision 1.4Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Revision 1.5May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Helicase SEN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,37366
Polymers85,1661
Non-polymers5,20765
Water19,6361090
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14100 Å2
ΔGint149 kcal/mol
Surface area30900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.830, 171.600, 69.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2378-

HOH

21A-3109-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Helicase SEN1 / tRNA-splicing endonuclease positive effector


Mass: 85166.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SEN1, YLR430W, L9576.1 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q00416, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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Non-polymers , 6 types, 1155 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1090 / 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: 3.2 Å3/Da / Density % sol: 61.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 18% PEG 2K 0.1M MOPS 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 2.7 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 12, 2016
RadiationMonochromator: Si (1,1,1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 23557 / % possible obs: 99.1 % / Redundancy: 49.12 % / CC1/2: 0.999 / Rrim(I) all: 0.0318 / Net I/σ(I): 31.08
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 37.88 % / Mean I/σ(I) obs: 1.66 / Num. unique obs: 1653 / CC1/2: 0.693 / Rrim(I) all: 0.4279 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.95→48.551 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.01
RfactorNum. reflection% reflection
Rfree0.2127 1177 5 %
Rwork0.1692 --
obs0.1714 23538 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.95→48.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5393 0 337 1090 6820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045770
X-RAY DIFFRACTIONf_angle_d0.6587656
X-RAY DIFFRACTIONf_dihedral_angle_d12.7173469
X-RAY DIFFRACTIONf_chiral_restr0.044832
X-RAY DIFFRACTIONf_plane_restr0.004955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.08430.55341380.51482651X-RAY DIFFRACTION96
3.0843-3.24680.26891440.23612727X-RAY DIFFRACTION98
3.2468-3.45020.22711450.15752744X-RAY DIFFRACTION99
3.4502-3.71650.22231460.15762770X-RAY DIFFRACTION99
3.7165-4.09040.19261470.13942812X-RAY DIFFRACTION100
4.0904-4.68180.1691480.12062812X-RAY DIFFRACTION100
4.6818-5.8970.19461500.15862850X-RAY DIFFRACTION100
5.897-48.5580.21941590.19152995X-RAY DIFFRACTION100

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