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- PDB-6l8k: Structure of URT1 in complex with UTP -

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Basic information

Entry
Database: PDB / ID: 6l8k
TitleStructure of URT1 in complex with UTP
ComponentsUTP:RNA uridylyltransferase 1
KeywordsTRANSFERASE / Uridylyltransferase / Complex
Function / homology
Function and homology information


negative regulation of post-transcriptional gene silencing by regulatory ncRNA / miRNA catabolic process / RNA 3' uridylation / 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
URIDINE 5'-TRIPHOSPHATE / UTP:RNA uridylyltransferase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.999 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
DepositionNov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8912
Polymers43,4071
Non-polymers4841
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-3 kcal/mol
Surface area16010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.766, 64.928, 66.371
Angle α, β, γ (deg.)90.000, 121.190, 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
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: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
Has ligand of interestN

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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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES PH7.5, 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: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.999→30.627 Å / Num. obs: 8925 / % possible obs: 98.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 65.73 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.857
Reflection shellResolution: 2.999→3.4 Å / Rmerge(I) obs: 0.499 / Num. unique obs: 2924

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5w0n

5w0n


Resolution: 2.999→30.627 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 24.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 430 4.82 %
Rwork0.1904 8495 -
obs0.1927 8925 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.39 Å2 / Biso mean: 61.8459 Å2 / Biso min: 27.94 Å2
Refinement stepCycle: final / Resolution: 2.999→30.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 29 0 2630
Biso mean--93.87 --
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022687
X-RAY DIFFRACTIONf_angle_d0.543650
X-RAY DIFFRACTIONf_chiral_restr0.043406
X-RAY DIFFRACTIONf_plane_restr0.004466
X-RAY DIFFRACTIONf_dihedral_angle_d16.9871618
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.999-3.43230.29771410.2483278398
3.4323-4.32240.23751440.1883283699
4.3224-30.6270.22011450.1717287698
Refinement TLS params.Method: refined / Origin x: 25.761 Å / Origin y: -0.8185 Å / Origin z: 18.1913 Å
111213212223313233
T0.3033 Å20.0343 Å20.0334 Å2-0.4257 Å2-0.0126 Å2--0.3412 Å2
L1.7574 °20.5872 °20.1355 °2-1.7135 °2-0.1328 °2--1.3481 °2
S-0.0418 Å °0.1107 Å °0.0111 Å °-0.0487 Å °-0.0882 Å °0.1415 Å °-0.0343 Å °-0.1492 Å °0.1317 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA426 - 755
2X-RAY DIFFRACTION1ALLA801

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