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- PDB-2q0g: Terminal uridylyl transferase 4 from Trypanosoma brucei with bound UPU -

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Basic information

Entry
Database: PDB / ID: 2q0g
TitleTerminal uridylyl transferase 4 from Trypanosoma brucei with bound UPU
ComponentsRNA uridylyl transferase
KeywordsTRANSFERASE / TUTase / Trypanosoma / nucleotidyltransferase / UTP-binding / RNA-editing
Function / homology
Function and homology information


RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / kinetoplast / nucleotide binding / mitochondrion / RNA binding / metal ion binding
Similarity search - Function
TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Chem-UPU / Terminal uridylyltransferase 4
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsStagno, J. / Luecke, H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Dual role of the RNA substrate in selectivity and catalysis by terminal uridylyl transferases.
Authors: Stagno, J. / Aphasizheva, I. / Aphasizhev, R. / Luecke, H.
History
DepositionMay 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 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 / struct_ref_seq_dif / struct_site
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_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.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_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA uridylyl transferase
B: RNA uridylyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9798
Polymers79,7592
Non-polymers1,2206
Water3,153175
1
A: RNA uridylyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4904
Polymers39,8791
Non-polymers6103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA uridylyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4904
Polymers39,8791
Non-polymers6103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.544, 41.953, 106.593
Angle α, β, γ (deg.)90.000, 95.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RNA uridylyl transferase / 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 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q381M1, RNA uridylyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-UPU / [(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-4-HYDROXY-2-(HYDROXYMETHYL)TETRAHYDROFURAN-3-YL HYDROGEN (S)-PHOSPHATE


Mass: 550.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H23N4O14P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate, 200 mM calcium acetate, 18% PEG-8000, 4 mM MgCl2, 50 uM UTP, crystals soaked in 10 mM UPU for 30 minutes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorDate: Nov 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→46.53 Å / Num. obs: 32493 / % possible obs: 99.9 % / Redundancy: 3.65 % / Rmerge(I) obs: 0.141 / Χ2: 0.99 / Net I/σ(I): 5.6 / Scaling rejects: 897
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.3-2.383.680.522.11177131991.06100
2.38-2.483.680.4842.21198032531.01100
2.48-2.593.690.4562.31175731800.99100
2.59-2.733.670.4242.61194632381.08100
2.73-2.93.70.3822.71186031911.0299.9
2.9-3.123.680.2933.41206932521.0299.9
3.12-3.443.650.1974.61199232530.9999.8
3.44-3.933.590.127.61184032440.9599.8
3.93-4.953.640.07412.11208432750.8999.9
4.95-46.533.530.05216.21217234080.8599.7

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Processing

Software
NameVersionClassificationNB
d*TREK9.2Ldata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
Blu-IceIcedata collection
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2IKF

2ikf


Resolution: 2.3→46.52 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.893 / SU B: 10.926 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.412 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1681 5.2 %test set taken from 2IKF
Rwork0.228 ---
obs0.231 32469 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.789 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.17 Å2
2---0.07 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5174 0 78 175 5427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225368
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9737294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5225645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33323.135252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.28115898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4431549
X-RAY DIFFRACTIONr_chiral_restr0.0980.2821
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024055
X-RAY DIFFRACTIONr_nbd_refined0.2130.22156
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23562
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2218
X-RAY DIFFRACTIONr_metal_ion_refined0.1360.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.25
X-RAY DIFFRACTIONr_mcbond_it0.7271.53325
X-RAY DIFFRACTIONr_mcangle_it1.28925238
X-RAY DIFFRACTIONr_scbond_it1.6532321
X-RAY DIFFRACTIONr_scangle_it2.5694.52056
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 124 -
Rwork0.288 2248 -
obs-2372 100 %

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