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- PDB-6l3f: The structure of UTP:RNA uridylyltransferase 1 (URT1) in in Arabi... -

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Basic information

Entry
Database: PDB / ID: 6l3f
TitleThe structure of UTP:RNA uridylyltransferase 1 (URT1) in in Arabidopsis
ComponentsUTP:RNA uridylyltransferase 1
KeywordsTRANSFERASE / Terminal uridylyltransferase
Function / homology
Function and homology information


negative regulation of post-transcriptional gene silencing by regulatory ncRNA / miRNA catabolic process / : / RNA uridylyltransferase / RNA uridylyltransferase activity / nuclear-transcribed mRNA poly(A) tail shortening / P-body / mRNA processing / mRNA binding / metal ion binding
Similarity search - Function
TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / : / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
UTP:RNA uridylyltransferase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.975 Å
AuthorsLingru, Z.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of Arabidopsis terminal uridylyl transferase URT1.
Authors: Zhu, L. / Hu, Q. / Cheng, L. / Jiang, Y. / Lv, M. / Liu, Y. / Li, F. / Shi, Y. / Gong, Q.
History
DepositionOct 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: UTP:RNA uridylyltransferase 1


Theoretical massNumber of molelcules
Total (without water)43,4071
Polymers43,4071
Non-polymers00
Water1,38777
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)123.320, 65.086, 66.115
Angle α, β, γ (deg.)90.000, 121.150, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein UTP:RNA uridylyltransferase 1


Mass: 43406.594 Da / Num. of mol.: 1 / Mutation: E6F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: URT1, At2g45620, F17K2.15 / Production host: Escherichia coli (E. coli) / References: UniProt: O64642, RNA uridylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.5,10% PEG6000,5% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 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: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.975→35.104 Å / Num. obs: 31325 / % possible obs: 99.13 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.91
Reflection shellResolution: 1.975→2.04 Å / Rmerge(I) obs: 0.421 / Num. unique obs: 31325

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Processing

Software
NameVersionClassification
PHENIX1.1refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W0N

5w0n


Resolution: 1.975→35.104 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 19.01
RfactorNum. reflection% reflection
Rfree0.1989 1590 5.08 %
Rwork0.1717 --
obs0.1732 31325 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.67 Å2 / Biso mean: 31.4698 Å2 / Biso min: 11.35 Å2
Refinement stepCycle: final / Resolution: 1.975→35.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 0 78 2696
Biso mean---29.72 -
Num. residues----322
LS refinement shellResolution: 1.975→2.0382 Å
RfactorNum. reflection
Rfree0.2216 119
Rwork0.1939 -
obs-2566
Refinement TLS params.Method: refined / Origin x: 26.1569 Å / Origin y: -0.7147 Å / Origin z: 18.4589 Å
111213212223313233
T0.1405 Å20.0175 Å2-0.0073 Å2-0.1559 Å20.0119 Å2--0.1253 Å2
L0.8747 °20.302 °2-0.1806 °2-0.4869 °2-0.0781 °2--0.4965 °2
S0.007 Å °0.1225 Å °0.0033 Å °-0.0181 Å °0.0001 Å °0.0322 Å °0.031 Å °-0.0687 Å °-0.007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA425 - 755
2X-RAY DIFFRACTION1allC1 - 101

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