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- PDB-5hzd: RNA Editing TUTase 1 from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 5hzd
TitleRNA Editing TUTase 1 from Trypanosoma brucei
Components3' terminal uridylyl transferase
KeywordsTRANSFERASE / RNA Editing TUTase1 / Trypanosoma brucei
Function / homology
Function and homology information


mitochondrial mRNA modification / RNA uridylyltransferase / RNA 3'-end processing / RNA uridylyltransferase activity / rRNA modification / protein homooligomerization / mRNA processing / nucleotide binding / protein-containing complex / mitochondrion ...mitochondrial mRNA modification / RNA uridylyltransferase / RNA 3'-end processing / RNA uridylyltransferase activity / rRNA modification / protein homooligomerization / mRNA processing / nucleotide binding / protein-containing complex / mitochondrion / RNA binding / zinc ion binding
Similarity search - Function
PAP/25A-associated / Cid1 family poly A polymerase / : / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Zinc finger C2H2 type domain profile. / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Terminal uridylyltransferase 1
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsThore, S. / Rajappa, L.T.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: RNA Editing TUTase 1: structural foundation of substrate recognition, complex interactions and drug targeting.
Authors: Rajappa-Titu, L. / Suematsu, T. / Munoz-Tello, P. / Long, M. / Demir, O. / Cheng, K.J. / Stagno, J.R. / Luecke, H. / Amaro, R.E. / Aphasizheva, I. / Aphasizhev, R. / Thore, S.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: 3' terminal uridylyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9455
Polymers57,6521
Non-polymers2934
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-26 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.800, 58.130, 66.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1230-

HOH

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Components

#1: Protein 3' terminal uridylyl transferase / RNA Editing TUTase1


Mass: 57651.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: 3' TUTase / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WQX5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.18 Å3/Da / Density % sol: 43.59 % / Description: Plates
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris pH8.5, 19% PEG 3350, 0.2M Lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 81270 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Biso Wilson estimate: 20.36 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.72
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.5-1.541.6441.58196.7
1.54-1.581.3032.111100
1.58-1.631.0742.61100
1.63-1.680.8113.571100
1.68-1.730.6454.651100
1.73-1.790.5085.861100
1.79-1.860.3837.671100
1.86-1.940.299.861100
1.94-2.020.19413.941100
2.02-2.120.15117.211100
2.12-2.240.11621.231100
2.24-2.370.09526.151100
2.37-2.540.07732.231100
2.54-2.740.06537.061100
2.74-30.05642.121100
3-3.350.04549.841100
3.35-3.870.03855.061100
3.87-4.740.03359.191100
4.74-6.710.03563.751100
6.710.02964.83199.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IKF

2ikf


Resolution: 1.6→24.646 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.25
RfactorNum. reflection% reflection
Rfree0.1996 3365 5 %
Rwork0.1659 --
obs0.1676 67307 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.28 Å2 / Biso mean: 24.14 Å2 / Biso min: 10.25 Å2
Refinement stepCycle: final / Resolution: 1.6→24.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 12 592 4418
Biso mean--52.91 34.81 -
Num. residues----476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014030
X-RAY DIFFRACTIONf_angle_d1.3135505
X-RAY DIFFRACTIONf_chiral_restr0.096608
X-RAY DIFFRACTIONf_plane_restr0.006708
X-RAY DIFFRACTIONf_dihedral_angle_d12.1961503
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.62290.27871400.238426532793
1.6229-1.64710.23661360.220525882724
1.6471-1.67280.21531400.198226532793
1.6728-1.70020.21541370.193326152752
1.7002-1.72950.22321390.195926352774
1.7295-1.7610.23361390.193426442783
1.761-1.79480.25881370.186326062743
1.7948-1.83150.22961390.182426332772
1.8315-1.87130.22481400.180426672807
1.8713-1.91480.23421380.175326182756
1.9148-1.96270.19821400.171226712811
1.9627-2.01570.21521390.173426252764
2.0157-2.0750.19741390.165626412780
2.075-2.14190.18151400.164726582798
2.1419-2.21840.20811390.162826582797
2.2184-2.30720.20251400.162226532793
2.3072-2.41210.21951400.164226512791
2.4121-2.53920.19981410.162226852826
2.5392-2.69810.22571400.167426562796
2.6981-2.90610.2021420.170327102852
2.9061-3.1980.20341410.163626772818
3.198-3.65940.16031440.151227322876
3.6594-4.60560.1861430.140227222865
4.6056-24.64850.18361520.172328913043
Refinement TLS params.Method: refined / Origin x: 93.6014 Å / Origin y: 138.0758 Å / Origin z: 51.2935 Å
111213212223313233
T0.1328 Å2-0.0158 Å2-0.0297 Å2-0.118 Å20.0026 Å2--0.1265 Å2
L0.6777 °2-0.1283 °2-0.3253 °2-0.4805 °20.1708 °2--0.5759 °2
S0.0434 Å °-0.058 Å °-0.0186 Å °-0.0612 Å °-0.0051 Å °-0.0187 Å °-0.0104 Å °0.0034 Å °0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA190 - 698
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allS1 - 603
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allD1
6X-RAY DIFFRACTION1allE1

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