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- PDB-5kal: Terminal uridylyl transferase 4 from Trypanosoma brucei with boun... -

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Basic information

Entry
Database: PDB / ID: 5kal
TitleTerminal uridylyl transferase 4 from Trypanosoma brucei with bound UTP and UpU
Components
  • RNA (5'-R(*UP*U)-3')
  • RNA uridylyltransferase 4
KeywordsTransferase/RNA / trypanosoma / RNA editing / TUTase / transferase / Transferase-RNA complex
Function / homology
Function and homology information


: / RNA uridylyltransferase / RNA 3'-end processing / RNA uridylyltransferase activity / kinetoplast / nucleotidyltransferase activity / nucleotide binding / mitochondrion / RNA binding / metal ion binding
Similarity search - Function
TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / : / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / RNA / Terminal uridylyltransferase 4 / Terminal uridylyltransferase 4
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsStagno, J.R. / Luecke, H. / Afasizhev, R.
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
DepositionJun 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA uridylyltransferase 4
B: RNA uridylyltransferase 4
Y: RNA (5'-R(*UP*U)-3')
Z: RNA (5'-R(*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,98311
Polymers80,8944
Non-polymers1,0907
Water3,423190
1
A: RNA uridylyltransferase 4
Y: RNA (5'-R(*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9805
Polymers40,4472
Non-polymers5333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-30 kcal/mol
Surface area16400 Å2
MethodPISA
2
B: RNA uridylyltransferase 4
Z: RNA (5'-R(*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0046
Polymers40,4472
Non-polymers5574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-39 kcal/mol
Surface area16180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.688, 42.876, 109.618
Angle α, β, γ (deg.)90.00, 94.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RNA uridylyltransferase 4


Mass: 39879.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: TUT4 / Production host: Escherichia coli (E. coli) / References: UniProt: A4UBD5, UniProt: Q381M1*PLUS
#2: RNA chain RNA (5'-R(*UP*U)-3')


Mass: 567.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Trypanosoma brucei (eukaryote)
#3: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


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


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


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM sodium cacodylate pH 6.5, 200mM calcium acetate, 18% PEG-8000, 5mM UTP, 5mM UpU

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→47.13 Å / Num. obs: 20369 / % possible obs: 99.5 % / Redundancy: 3.52 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 7.1
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 3.48 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(dev-2447_1692: ???)refinement
d*TREKdata scaling
PDB_EXTRACT3.2data extraction
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IKF

2ikf


Resolution: 2.75→47.129 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.259 1070 5.26 %
Rwork0.2136 --
obs0.216 20345 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→47.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5115 74 63 190 5442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145428
X-RAY DIFFRACTIONf_angle_d0.5667358
X-RAY DIFFRACTIONf_dihedral_angle_d10.8913246
X-RAY DIFFRACTIONf_chiral_restr0.043827
X-RAY DIFFRACTIONf_plane_restr0.003931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.87520.44291340.33282389X-RAY DIFFRACTION100
2.8752-3.02670.34111250.30062403X-RAY DIFFRACTION100
3.0267-3.21630.35571420.28942366X-RAY DIFFRACTION100
3.2163-3.46460.29841450.24072374X-RAY DIFFRACTION100
3.4646-3.81310.2491290.20012411X-RAY DIFFRACTION100
3.8131-4.36450.22261330.16982433X-RAY DIFFRACTION100
4.3645-5.49750.18241250.15932390X-RAY DIFFRACTION98
5.4975-47.13560.23161370.20472509X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 23.1549 Å / Origin y: 26.5803 Å / Origin z: -69.644 Å
111213212223313233
T0.1661 Å20.0165 Å20.0413 Å2-0.1747 Å2-0.006 Å2--0.2623 Å2
L0.5192 °2-0.1128 °20.5518 °2-0.7617 °2-0.319 °2--1.8922 °2
S0.0363 Å °0.0867 Å °0.0307 Å °-0.1314 Å °-0.0301 Å °0.0054 Å °-0.0717 Å °0.0687 Å °-0.0172 Å °
Refinement TLS groupSelection details: all

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