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- PDB-2q0d: Terminal uridylyl transferase 4 from Trypanosoma brucei with bound ATP -

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Basic information

Entry
Database: PDB / ID: 2q0d
TitleTerminal uridylyl transferase 4 from Trypanosoma brucei with bound ATP
ComponentsRNA uridylyl transferase
KeywordsTRANSFERASE / TUTase / Trypanosoma / nucleotidyltransferase / UTP-binding / RNA-editing
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
ADENOSINE-5'-TRIPHOSPHATE / Terminal uridylyltransferase 4
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)80,3155
Polymers79,7592
Non-polymers5563
Water4,756264
1
A: RNA uridylyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4354
Polymers39,8791
Non-polymers5563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA uridylyl transferase


Theoretical massNumber of molelcules
Total (without water)39,8791
Polymers39,8791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.190, 41.970, 106.420
Angle α, β, γ (deg.)90.000, 94.010, 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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
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 ATP, 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: Jul 4, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→42.87 Å / Num. obs: 48171 / % possible obs: 99.5 % / Redundancy: 3.56 % / Rmerge(I) obs: 0.092 / Χ2: 0.99 / Net I/σ(I): 8.5 / Scaling rejects: 1298
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2-2.073.270.4632.31536346461.2297.4
2.07-2.153.640.4242.71757047871.1599.8
2.15-2.253.630.3732.91734647481.1199.5
2.25-2.373.590.3063.51744248191.199.6
2.37-2.523.60.25541751048251.0399.9
2.52-2.713.60.2074.71735647900.9899.9
2.71-2.993.620.1516.21764748460.9599.9
2.99-3.423.620.08810.11760548380.8599.9
3.42-4.313.580.04618.61761648710.8299.6
4.31-42.873.480.02829.41751350010.7699

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Processing

Software
NameVersionClassificationNB
d*TREK9.2Ldata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
Blu-IceIcedata collection
d*TREKdata reduction
CCP4suitephasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2IKF

2ikf


Resolution: 2→35.38 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.002 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2473 5.1 %Test set taken from 2IKF
Rwork0.221 ---
obs0.222 48158 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.652 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20.24 Å2
2---0.35 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→35.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5163 0 33 264 5460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225309
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.9617211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1795643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6923.294252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87815890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4281546
X-RAY DIFFRACTIONr_chiral_restr0.1050.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024019
X-RAY DIFFRACTIONr_nbd_refined0.2040.22328
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23558
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2320
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2770.213
X-RAY DIFFRACTIONr_mcbond_it0.941.53335
X-RAY DIFFRACTIONr_mcangle_it1.51625226
X-RAY DIFFRACTIONr_scbond_it2.1232259
X-RAY DIFFRACTIONr_scangle_it3.2374.51985
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 179 -
Rwork0.285 3236 -
obs-3415 96.5 %

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