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- PDB-5z4m: Structure of TailorD343A with bound UTP and Mg -

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Basic information

Entry
Database: PDB / ID: 5z4m
TitleStructure of TailorD343A with bound UTP and Mg
ComponentsTerminal uridylyltransferase Tailor
KeywordsTRANSFERASE / Terminal uridylyltransferase
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
URIDINE 5'-TRIPHOSPHATE / Terminal uridylyltransferase Tailor
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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

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Assembly

Deposited unit
A: Terminal uridylyltransferase Tailor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6514
Polymers41,6581
Non-polymers9933
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-16 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.962, 84.556, 149.347
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-817-

HOH

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Components

#1: Protein Terminal uridylyltransferase Tailor / TUTase Tailor


Mass: 41658.449 Da / Num. of mol.: 1 / Mutation: D343A
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: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 47.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium 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: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 40441 / % possible obs: 99.7 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.02 / Rrim(I) all: 0.074 / Χ2: 0.891 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.74-1.7711.50.5919640.9460.1750.6170.48998.9
1.77-1.811.30.54419900.9630.1640.5690.49299
1.8-1.8412.10.44520010.9820.1310.4640.505100
1.84-1.8713.40.42220210.9830.1190.4390.513100
1.87-1.9213.50.34519590.9880.0970.3590.535100
1.92-1.9613.50.320320.9910.0840.3110.559100
1.96-2.0113.40.24920260.9930.070.2590.583100
2.01-2.0613.10.20519830.9930.0580.2130.6299.9
2.06-2.1212.90.1820000.9950.0520.1880.691100
2.12-2.1911.90.14920030.9950.0440.1560.7599.4
2.19-2.2713.70.13120310.9970.0370.1360.786100
2.27-2.3613.70.11220180.9970.0310.1170.797100
2.36-2.4713.50.120200.9980.0280.1040.866100
2.47-2.613.40.09120310.9980.0260.0950.94799.9
2.6-2.7612.80.07820190.9980.0220.0811.04999.4
2.76-2.9813.10.0720020.9980.020.0731.24198.7
2.98-3.2713.70.06520670.9980.0180.0681.457100
3.27-3.7513.30.05820520.9990.0160.061.648100
3.75-4.7212.50.0520580.9990.0140.0521.69599
4.72-5012.30.04621640.9980.0140.0481.42398.9

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Processing

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

4nkt


Resolution: 1.74→30.981 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.33
RfactorNum. reflection% reflection
Rfree0.2061 1998 4.95 %
Rwork0.1673 --
obs0.1692 40325 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 215.05 Å2 / Biso mean: 46.7466 Å2 / Biso min: 17.2 Å2
Refinement stepCycle: final / Resolution: 1.74→30.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 0 81 177 3060
Biso mean--68.81 39.66 -
Num. residues----350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012928
X-RAY DIFFRACTIONf_angle_d1.0433986
X-RAY DIFFRACTIONf_chiral_restr0.06451
X-RAY DIFFRACTIONf_plane_restr0.007496
X-RAY DIFFRACTIONf_dihedral_angle_d14.1631739
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7404-1.78390.30331160.28172647276397
1.7839-1.83210.33161390.255126962835100
1.8321-1.88610.31311410.234127562897100
1.8861-1.94690.27641390.218427372876100
1.9469-2.01650.24821330.190627242857100
2.0165-2.09720.21571540.183927202874100
2.0972-2.19260.23011530.183626892842100
2.1926-2.30820.19081450.174327442889100
2.3082-2.45280.2151270.171227532880100
2.4528-2.6420.2171470.174327652912100
2.642-2.90770.23071610.17272710287199
2.9077-3.32810.19141560.168827502906100
3.3281-4.19140.1811340.14632795292999
4.1914-30.98590.17361530.13992841299497
Refinement TLS params.Method: refined / Origin x: -3.9787 Å / Origin y: -24.7454 Å / Origin z: 16.1791 Å
111213212223313233
T0.2229 Å2-0.0706 Å2-0.0205 Å2-0.2035 Å20.0056 Å2--0.1981 Å2
L1.8985 °2-0.3726 °20.3975 °2-0.693 °2-0.6315 °2--2.0832 °2
S-0.0186 Å °0.301 Å °0.0747 Å °0.0311 Å °0.0108 Å °0.0319 Å °-0.0013 Å °0.1551 Å °-0.0049 Å °
Refinement TLS groupSelection details: all

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