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- PDB-5ido: RNA Editing TUTase 1 from Trypanosoma brucei in complex with UTP -

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Basic information

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


mitochondrial mRNA modification / RNA 3' uridylation / RNA uridylyltransferase / rRNA modification / RNA uridylyltransferase activity / : / protein homooligomerization / nucleotide binding / protein-containing complex / mitochondrion ...mitochondrial mRNA modification / RNA 3' uridylation / RNA uridylyltransferase / rRNA modification / RNA uridylyltransferase activity / : / protein homooligomerization / nucleotide binding / protein-containing complex / mitochondrion / RNA binding / metal ion binding
Similarity search - Function
PAP/25A-associated / Cid1 family poly A polymerase / Zinc finger C2H2 type domain profile. / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / Terminal uridylyltransferase 1
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 24, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3' terminal uridylyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1814
Polymers57,6081
Non-polymers5743
Water3,081171
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-12 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.350, 66.340, 128.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein 3' terminal uridylyl transferase


Mass: 57607.516 Da / Num. of mol.: 1 / Fragment: residues 189-699
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-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.2 Å3/Da / Density % sol: 44.16 % / Description: Plates
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris pH8.5, between 5% and 8% PEG 3350, 0.2M Lithium chloride.Complex of D473A with UTP was obtained by soaking 1.5mM UTP supplemented with 1mM MgCl2

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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: Dec 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→19.72 Å / Num. obs: 26453 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Biso Wilson estimate: 37.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Net I/σ(I): 22.88
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.2-2.260.6543.91199.8
2.26-2.320.6694.04199.4
2.32-2.390.4236.85199.9
2.39-2.460.3159.071100
2.46-2.540.26210.51199.9
2.54-2.630.20412.25199.9
2.63-2.730.16215.57199.9
2.73-2.840.1317.2199.6
2.84-2.970.10323.071100
2.97-3.110.08627.021100
3.11-3.280.06932.35199.9
3.28-3.480.06233.05199.7
3.48-3.720.05535.69199.3
3.72-4.020.04844.39199.9
4.02-4.40.04246.63199.4
4.4-4.920.04143.32199.4
4.92-5.680.04145.31198.5
5.68-6.960.0452.33198
6.96-9.840.03254.33196.4
9.840.03253.95182

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HZD

5hzd


Resolution: 2.2→19.727 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.92
RfactorNum. reflection% reflection
Rfree0.2879 1318 4.99 %
Rwork0.2478 --
obs0.2498 26391 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.33 Å2 / Biso mean: 42.0798 Å2 / Biso min: 16.15 Å2
Refinement stepCycle: final / Resolution: 2.2→19.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3773 0 31 171 3975
Biso mean--49.35 41.65 -
Num. residues----471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033899
X-RAY DIFFRACTIONf_angle_d0.7785305
X-RAY DIFFRACTIONf_chiral_restr0.03581
X-RAY DIFFRACTIONf_plane_restr0.003678
X-RAY DIFFRACTIONf_dihedral_angle_d14.4221425
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2880.3371460.26712760290699
2.288-2.39190.28981430.259327232866100
2.3919-2.51780.33461440.264327412885100
2.5178-2.67520.32461450.291427802925100
2.6752-2.88120.35161460.290627682914100
2.8812-3.17010.31951470.278927882935100
3.1701-3.62630.31241460.251927812927100
3.6263-4.55940.26791480.231328392987100
4.5594-19.72810.22961530.21242893304698
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0273-0.0379-0.056-0.01390.09420.18010.1411-0.1297-0.31830.0628-0.3787-0.041-0.1305-0.002500.16340.0449-0.05250.0495-0.09920.0168140.868690.643823.9079
20.00510.0013-0.00160.004-0.0001-0.0007-0.020.041-0.03-0.0185-0.04830.0412-0.0018-0.081800.1565-0.0599-0.01230.174-0.00150.25126.374474.765140.3773
30.041-0.0096-0.11680.0095-0.02510.0526-0.0209-0.005-0.12-0.0124-0.1058-0.11420.01770.0282-00.1072-0.0245-0.02170.10430.01620.134142.565174.826638.2901
40.03460.0187-0.02960.0105-0.06250.0805-0.0336-0.0322-0.1243-0.0342-0.0256-0.1134-0.2608-0.1541-00.22330.0421-0.04830.2034-0.04430.1587141.32296.079813.6351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 190 through 329 )A190 - 329
2X-RAY DIFFRACTION2chain 'A' and (resid 330 through 360 )A330 - 360
3X-RAY DIFFRACTION3chain 'A' and (resid 361 through 571 )A361 - 571
4X-RAY DIFFRACTION4chain 'A' and (resid 572 through 688 )A572 - 688

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