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- PDB-5uqj: Structure of yeast Usb1 -

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Basic information

Entry
Database: PDB / ID: 5uqj
TitleStructure of yeast Usb1
ComponentsU6 snRNA phosphodiesterase
KeywordsHYDROLASE / U6 snRNA 3' exonuclease Usb1 2H Phosphoesterase
Function / homology
Function and homology information


poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends / 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity / U6 snRNA 3'-end processing / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / Lyases; Phosphorus-oxygen lyases / 3'-5'-RNA exonuclease activity / lyase activity / mitochondrion / nucleus / cytoplasm
Similarity search - Function
U6 snRNA phosphodiesterase 1 / Uncharacterised conserved protein
Similarity search - Domain/homology
ACETATE ION / U6 snRNA phosphodiesterase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsDidychuk, A.L. / Montemayor, E.J. / Butcher, S.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118131 United States
CitationJournal: Nat Commun / Year: 2017
Title: Usb1 controls U6 snRNP assembly through evolutionarily divergent cyclic phosphodiesterase activities.
Authors: Didychuk, A.L. / Montemayor, E.J. / Carrocci, T.J. / DeLaitsch, A.T. / Lucarelli, S.E. / Westler, W.M. / Brow, D.A. / Hoskins, A.A. / Butcher, S.E.
History
DepositionFeb 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U6 snRNA phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5188
Polymers25,8871
Non-polymers6317
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: U6 snRNA phosphodiesterase
hetero molecules

A: U6 snRNA phosphodiesterase
hetero molecules

A: U6 snRNA phosphodiesterase
hetero molecules

A: U6 snRNA phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,07332
Polymers103,5474
Non-polymers2,52628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_556y,x,-z+11
Buried area9910 Å2
ΔGint-291 kcal/mol
Surface area43150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.850, 157.850, 44.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-305-

SO4

21A-442-

HOH

31A-466-

HOH

41A-468-

HOH

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Components

#1: Protein U6 snRNA phosphodiesterase / U six biogenesis protein 1


Mass: 25886.811 Da / Num. of mol.: 1 / Fragment: UNP residues 71-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: USB1, YLR132C, L3127 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) STAR pLysS
References: UniProt: Q12208, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 2 M ammonium sulfate, 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.8→49.917 Å / Num. obs: 49463 / % possible obs: 99.4 % / Redundancy: 14.6 % / Biso Wilson estimate: 28.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09 / Net I/σ(I): 23.3
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 14.1 % / Rmerge(I) obs: 2.23 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1517 / CC1/2: 0.446 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
RESOLVEmodel building
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→49.917 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 24.39
RfactorNum. reflection% reflection
Rfree0.2245 3798 7.68 %
Rwork0.1865 --
obs0.1895 49463 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→49.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 35 116 1877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181819
X-RAY DIFFRACTIONf_angle_d1.6812467
X-RAY DIFFRACTIONf_dihedral_angle_d14.719682
X-RAY DIFFRACTIONf_chiral_restr0.087266
X-RAY DIFFRACTIONf_plane_restr0.008315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7989-1.82170.38481370.3411663X-RAY DIFFRACTION98
1.8217-1.84570.26411380.31281685X-RAY DIFFRACTION97
1.8457-1.87090.2791410.28271650X-RAY DIFFRACTION99
1.8709-1.89770.3321360.27091735X-RAY DIFFRACTION100
1.8977-1.9260.32431430.27011673X-RAY DIFFRACTION97
1.926-1.95610.27091350.2621656X-RAY DIFFRACTION100
1.9561-1.98820.26121420.25591714X-RAY DIFFRACTION100
1.9882-2.02250.28331410.23871678X-RAY DIFFRACTION98
2.0225-2.05920.2931410.2381660X-RAY DIFFRACTION100
2.0592-2.09880.29341430.24061732X-RAY DIFFRACTION100
2.0988-2.14170.2731360.2241642X-RAY DIFFRACTION98
2.1417-2.18830.28361410.21271713X-RAY DIFFRACTION100
2.1883-2.23920.23471430.20691698X-RAY DIFFRACTION99
2.2392-2.29520.24181340.19551681X-RAY DIFFRACTION100
2.2952-2.35720.21811420.19381708X-RAY DIFFRACTION99
2.3572-2.42660.271410.18981695X-RAY DIFFRACTION100
2.4266-2.50490.23781410.19021688X-RAY DIFFRACTION99
2.5049-2.59440.22011410.18891704X-RAY DIFFRACTION100
2.5944-2.69830.25491430.18491675X-RAY DIFFRACTION99
2.6983-2.82110.18791390.18231709X-RAY DIFFRACTION100
2.8211-2.96980.25681410.18321718X-RAY DIFFRACTION100
2.9698-3.15580.22141470.16841689X-RAY DIFFRACTION100
3.1558-3.39940.21981420.1691685X-RAY DIFFRACTION100
3.3994-3.74140.18981480.15011701X-RAY DIFFRACTION100
3.7414-4.28260.1631390.14421681X-RAY DIFFRACTION100
4.2826-5.39460.18451470.14681719X-RAY DIFFRACTION100
5.3946-49.93580.2161360.20211713X-RAY DIFFRACTION100

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