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- PDB-6i0s: Crystal structure of DmTailor in complex with UMPNPP -

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Basic information

Entry
Database: PDB / ID: 6i0s
TitleCrystal structure of DmTailor in complex with UMPNPP
ComponentsTerminal uridylyltransferase Tailor
KeywordsTRANSFERASE / Terminal uridyl transferase / nucleotidyl transferase
Function / homology
Function and homology information


negative regulation of pre-miRNA processing / positive regulation of miRNA catabolic process / RNA uridylyltransferase / RNA uridylyltransferase activity / regulatory ncRNA-mediated gene silencing / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Cid1 family poly A polymerase / : / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Chem-2KH / Terminal uridylyltransferase Tailor
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKroupova, A. / Ivascu, A. / Jinek, M.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural basis for acceptor RNA substrate selectivity of the 3' terminal uridylyl transferase Tailor.
Authors: Kroupova, A. / Ivascu, A. / Reimao-Pinto, M.M. / Ameres, S.L. / Jinek, M.
History
DepositionOct 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_struct_ref_seq_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
Revision 1.2Jan 24, 2024Group: 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: Terminal uridylyltransferase Tailor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7673
Polymers44,2591
Non-polymers5072
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area16530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.183, 61.183, 167.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Terminal uridylyltransferase Tailor / TUTase Tailor


Mass: 44259.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Tailor, CG1091 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9VI58, RNA uridylyltransferase
#2: Chemical ChemComp-2KH / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20 % (v/v) glycerol ethoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00767 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00767 Å / Relative weight: 1
ReflectionResolution: 1.9→44.77 Å / Num. obs: 29527 / % possible obs: 100 % / Redundancy: 19.6 % / CC1/2: 0.999 / Rsym value: 0.119 / Net I/σ(I): 15.81
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 19 % / Mean I/σ(I) obs: 1.4 / CC1/2: 0.534 / Rsym value: 1.55 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
PHASERphasing
Cootmodel building
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W0B

5w0b


Resolution: 1.9→44.768 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9
RfactorNum. reflection% reflection
Rfree0.2188 1487 5.04 %
Rwork0.1882 --
obs0.1897 29527 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→44.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 30 221 3045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112888
X-RAY DIFFRACTIONf_angle_d0.8843918
X-RAY DIFFRACTIONf_dihedral_angle_d25.1911070
X-RAY DIFFRACTIONf_chiral_restr0.053442
X-RAY DIFFRACTIONf_plane_restr0.005491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8998-1.96110.27751320.27972494X-RAY DIFFRACTION100
1.9611-2.03120.23361370.2432504X-RAY DIFFRACTION100
2.0312-2.11250.2431230.22122518X-RAY DIFFRACTION100
2.1125-2.20860.22761370.20732507X-RAY DIFFRACTION100
2.2086-2.32510.24871410.19822499X-RAY DIFFRACTION100
2.3251-2.47070.241320.19562523X-RAY DIFFRACTION100
2.4707-2.66150.22711340.1932556X-RAY DIFFRACTION100
2.6615-2.92930.21541330.1862530X-RAY DIFFRACTION100
2.9293-3.3530.2321340.18542555X-RAY DIFFRACTION100
3.353-4.2240.20431380.16252608X-RAY DIFFRACTION100
4.224-44.78030.19491460.18192746X-RAY DIFFRACTION100

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