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- PDB-5z4a: Structure of Tailor in complex with AGU RNA -

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Basic information

Entry
Database: PDB / ID: 5z4a
TitleStructure of Tailor in complex with AGU RNA
Components
  • RNA (5'-R(*AP*GP*U)-3')
  • Terminal uridylyltransferase Tailor
KeywordsTRANSFERASE/RNA / Terminal uridylyltransferase / TRANSFERASE-RNA complex
Function / homology
Function and homology information


positive regulation of miRNA catabolic process / RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / pre-miRNA processing / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Cid1 family poly A polymerase / 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: 1.637 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 10, 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
B: RNA (5'-R(*AP*GP*U)-3')
A: Terminal uridylyltransferase Tailor


Theoretical massNumber of molelcules
Total (without water)41,3262
Polymers41,3262
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-7 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.717, 84.944, 148.262
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-765-

HOH

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Components

#1: RNA chain RNA (5'-R(*AP*GP*U)-3')


Mass: 935.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#2: Protein Terminal uridylyltransferase Tailor / TUTase Tailor


Mass: 40390.020 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
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: 1.637→50 Å / Num. obs: 48194 / % possible obs: 99.5 % / Redundancy: 12.8 % / Biso Wilson estimate: 19.75 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.025 / Rrim(I) all: 0.089 / Χ2: 0.601 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.86-1.8910.80.49314420.9480.1490.5150.46393.1
1.89-1.9311.30.48916070.9480.1450.5110.46997.3
1.93-1.9611.70.43115640.9730.1270.4490.4898.7
1.96-212.10.37816100.9740.1110.3940.48299.9
2-2.0512.50.31815930.9790.0930.3320.49100
2.05-2.0912.70.2916060.9870.0840.3030.499100
2.09-2.1512.20.25616180.9880.0760.2670.497100
2.15-2.2112.70.21916080.990.0640.2280.508100
2.21-2.2713.60.19716180.9930.0550.2050.541100
2.27-2.3413.80.17216050.9940.0480.1790.538100
2.34-2.4313.60.15415950.9950.0430.160.56100
2.43-2.5213.70.13816360.9950.0390.1440.562100
2.52-2.6413.40.12116170.9970.0340.1260.597100
2.64-2.7812.60.10316220.9970.030.1080.643100
2.78-2.9513.20.0916340.9980.0260.0940.66999.9
2.95-3.1813.90.08116260.9980.0220.0840.697100
3.18-3.513.60.07116560.9980.020.0730.754100
3.5-4.0112.70.06216610.9980.0180.0650.835100
4.01-5.0513.20.05716560.9980.0160.0590.822100
5.05-5012.30.05517710.9990.0160.0570.79100

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Processing

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

4nkt


Resolution: 1.637→49.93 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.93
RfactorNum. reflection% reflection
Rfree0.1905 2419 5.02 %
Rwork0.1571 --
obs0.1587 48194 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 168.58 Å2 / Biso mean: 32.491 Å2 / Biso min: 11.77 Å2
Refinement stepCycle: final / Resolution: 1.637→49.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2829 62 0 243 3134
Biso mean---32.88 -
Num. residues----354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093016
X-RAY DIFFRACTIONf_angle_d0.9794109
X-RAY DIFFRACTIONf_chiral_restr0.059463
X-RAY DIFFRACTIONf_plane_restr0.007516
X-RAY DIFFRACTIONf_dihedral_angle_d14.4161822
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6372-1.67060.21061250.19892547267296
1.6706-1.7070.24751540.191426582812100
1.707-1.74670.22541550.184826762831100
1.7467-1.79030.20831400.179826342774100
1.7903-1.83880.20561310.171226792810100
1.8388-1.89290.21781520.175826762828100
1.8929-1.9540.20451350.167326932828100
1.954-2.02380.18661280.162127112839100
2.0238-2.10480.19531300.160326902820100
2.1048-2.20060.1891540.159126632817100
2.2006-2.31660.17661480.156326822830100
2.3166-2.46180.17641430.151326882831100
2.4618-2.65190.18981630.158126952858100
2.6519-2.91870.20151370.157127432880100
2.9187-3.3410.1951430.159627012844100
3.341-4.20890.18121470.140327602907100
4.2089-49.95290.17511340.149928793013100
Refinement TLS params.Method: refined / Origin x: -3.9806 Å / Origin y: -25.4418 Å / Origin z: 15.7645 Å
111213212223313233
T0.135 Å2-0.0462 Å2-0.0136 Å2-0.1528 Å2-0.0027 Å2--0.1095 Å2
L1.194 °2-0.0622 °20.0946 °2-0.6168 °2-0.4657 °2--1.5044 °2
S-0.0012 Å °0.1029 Å °0.0023 Å °0.0042 Å °0.0109 Å °0.0202 Å °0.0453 Å °0.0595 Å °-0.005 Å °
Refinement TLS groupSelection details: all

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