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- PDB-3hj1: Minor Editosome-Associated TUTase 1 with bound UTP -

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Basic information

Entry
Database: PDB / ID: 3hj1
TitleMinor Editosome-Associated TUTase 1 with bound UTP
ComponentsMinor Editosome-Associated TUTase
KeywordsTRANSFERASE / TUTase / nucleotidyltransferase / trypanosoma / editosome / RNA editing / UTP-binding
Function / homology
Function and homology information


RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / nuclear lumen / ciliary plasm / DNA-templated transcription / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Poly(a)-polymerase, middle domain - #10 / Poly(a)-polymerase, middle domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / RNA uridylyltransferase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsStagno, J. / Luecke, H.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure of the Mitochondrial Editosome-Like Complex Associated TUTase 1 Reveals Divergent Mechanisms of UTP Selection and Domain Organization.
Authors: Stagno, J. / Aphasizheva, I. / Bruystens, J. / Luecke, H. / Aphasizhev, R.
History
DepositionMay 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 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 / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

Downloads & links

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Assembly

Deposited unit
A: Minor Editosome-Associated TUTase
B: Minor Editosome-Associated TUTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0114
Polymers89,0432
Non-polymers9682
Water10,215567
1
A: Minor Editosome-Associated TUTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0062
Polymers44,5221
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Minor Editosome-Associated TUTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0062
Polymers44,5221
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.873, 101.999, 66.124
Angle α, β, γ (deg.)90.000, 111.650, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 1 / Auth seq-ID: 1 - 382 / Label seq-ID: 3 - 384

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit related by 2-fold non-crystallographic symmetry (chains A & B)

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Components

#1: Protein Minor Editosome-Associated TUTase


Mass: 44521.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb927.1.1330 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4GZ86
#2: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 567 / 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 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 291 K / pH: 8
Details: 0.2M lithium acetate, 25% PEG 3350, 0.5mM UTP, pH 8.0, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 54366 / % possible obs: 96.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 12.528
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.49 / % possible all: 83.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.69 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å31.05 Å
Translation2.5 Å31.05 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.2phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→31.05 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.658 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2782 5.1 %RANDOM
Rwork0.204 ---
obs0.206 54332 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å23.39 Å2
2---2.18 Å20 Å2
3---2.76 Å2
Refinement stepCycle: LAST / Resolution: 1.95→31.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6235 0 58 567 6860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216471
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9558757
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3345779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60723.075335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.707151118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.721562
X-RAY DIFFRACTIONr_chiral_restr0.0920.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214980
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6141.53855
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22226239
X-RAY DIFFRACTIONr_scbond_it2.31332616
X-RAY DIFFRACTIONr_scangle_it3.9514.52513
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3097 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.080.05
2Btight thermal0.130.5
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 186 -
Rwork0.283 3201 -
obs--81.46 %
Refinement TLS params.

T11: 0.0436 Å2 / 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 °)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4090.0959-0.27970.3148-0.17760.30430.0178-0.00060.02270.01620.00170.0294-0.0246-0.0202-0.0195-0.0003-0.02470.0437-0.0050.020859.734114.29732.3179
20.42720.1367-0.24760.2314-0.07870.29490.00120.0119-0.02120.0114-0.0122-0.0052-0.00840.01180.0110.0012-0.0260.0433-0.00290.017122.940738.875528.7532
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 382
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION1A407 - 683
4X-RAY DIFFRACTION2B-1 - 385
5X-RAY DIFFRACTION2B502
6X-RAY DIFFRACTION2B407 - 698

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