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- PDB-5z4d: Structure of Tailor in complex with AGUU RNA -

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Basic information

Entry
Database: PDB / ID: 5z4d
TitleStructure of Tailor in complex with AGUU RNA
Components
  • RNA (5'-R(*AP*GP*UP*U)-3')
  • Terminal uridylyltransferase Tailor
KeywordsTRANSFERASE/RNA / Terminal uridylyltransferase / TRANSFERASE-RNA complex
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
RNA / Terminal uridylyltransferase Tailor
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsCheng, L. / Li, F. / Jiang, Y. / Yu, H. / Xie, C. / Shi, Y. / Gong, Q.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural insights into a unique preference for 3' terminal guanine of mirtron in Drosophila TUTase tailor.
Authors: Cheng, L. / Li, F. / Jiang, Y. / Yu, H. / Xie, C. / Shi, Y. / Gong, Q.
History
DepositionJan 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
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 1.2Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
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

Downloads & links

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Assembly

Deposited unit
A: Terminal uridylyltransferase Tailor
B: RNA (5'-R(*AP*GP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)42,9442
Polymers42,9442
Non-polymers00
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-14 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.571, 84.787, 148.118
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-723-

HOH

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Components

#1: Protein Terminal uridylyltransferase Tailor / TUTase Tailor


Mass: 41702.457 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: Escherichia coli (E. coli) / References: UniProt: Q9VI58, RNA uridylyltransferase
#2: RNA chain RNA (5'-R(*AP*GP*UP*U)-3')


Mass: 1241.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium chloride, 0.1M Tris pH 8.4, 15% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 35714 / % possible obs: 98.9 % / Redundancy: 12.5 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.023 / Rrim(I) all: 0.083 / Χ2: 0.657 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8311.10.46516700.9540.1410.4870.50395.3
1.83-1.8611.60.43417430.9570.1290.4530.50395.8
1.86-1.911.70.37416870.9730.1110.390.55497.9
1.9-1.9412.40.35617680.9730.1020.3710.53197.1
1.94-1.9812.70.29717350.9820.0850.3090.5798.3
1.98-2.0312.60.25317690.9840.0720.2640.56898.7
2.03-2.0812.50.21717610.9850.0630.2260.59898.8
2.08-2.1312.60.19617630.9880.0560.2050.61898.9
2.13-2.212.60.1717890.9910.0490.1770.63499.4
2.2-2.2712.30.1518030.9930.0440.1560.672100
2.27-2.3511.70.13217690.9930.0390.1380.67799.5
2.35-2.4412.20.11817700.9960.0340.1230.68799.6
2.44-2.5513.10.11118050.9950.0320.1160.6699.9
2.55-2.6913.20.09617890.9970.0270.10.67899.7
2.69-2.8613.10.08418150.9970.0240.0880.71799.9
2.86-3.0812.90.07618390.9970.0220.0790.72599.9
3.08-3.3912.30.06717920.9980.020.070.77799.9
3.39-3.88130.0618360.9980.0170.0630.822100
3.88-4.8813.60.05818530.9980.0160.060.889100
4.88-5012.10.04919580.9990.0140.0510.644100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(1.10_2155: ???)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NKT

4nkt


Resolution: 1.803→49.82 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.35
RfactorNum. reflection% reflection
Rfree0.1843 1816 5.09 %
Rwork0.1575 --
obs0.1589 35660 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.82 Å2 / Biso mean: 34.4815 Å2 / Biso min: 12.76 Å2
Refinement stepCycle: final / Resolution: 1.803→49.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 82 0 186 3090
Biso mean---33.36 -
Num. residues----355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013020
X-RAY DIFFRACTIONf_angle_d1.0094118
X-RAY DIFFRACTIONf_chiral_restr0.06468
X-RAY DIFFRACTIONf_plane_restr0.007512
X-RAY DIFFRACTIONf_dihedral_angle_d14.5761819
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8032-1.8520.24451220.21192432255493
1.852-1.90650.2071380.18642479261797
1.9065-1.9680.19961390.17572563270298
1.968-2.03830.21491390.16222579271899
2.0383-2.120.20431420.15742574271699
2.12-2.21640.18671610.1532575273699
2.2164-2.33330.19091340.153225982732100
2.3333-2.47950.21081410.1526392780100
2.4795-2.67090.20251380.157826402778100
2.6709-2.93970.18071410.155826262767100
2.9397-3.3650.19651540.161926312785100
3.365-4.23920.15761290.145727112840100
4.2392-49.83950.16361380.158327972935100
Refinement TLS params.Method: refined / Origin x: 65.6536 Å / Origin y: 110.3443 Å / Origin z: 15.8729 Å
111213212223313233
T0.1536 Å2-0.0383 Å20.0122 Å2-0.1467 Å20.0031 Å2--0.1484 Å2
L1.4348 °20.0187 °2-0.0529 °2-0.7449 °20.4293 °2--1.5978 °2
S-0.0026 Å °0.1093 Å °-0.0161 Å °0.0022 Å °0.0025 Å °-0.0156 Å °-0.0385 Å °-0.0492 Å °0.0019 Å °
Refinement TLS groupSelection details: all

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