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- PDB-5gmc: Methylation at position 32 of tRNA catalyzed by TrmJ alters oxida... -

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Basic information

Entry
Database: PDB / ID: 5gmc
TitleMethylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruiginosa
ComponentstRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ
KeywordsTRANSFERASE / Pseudomonas aeruginosa / tRNA methyltransferase / TrmJ / oxidative stress / tRNA modification / wobble base
Function / homology
Function and homology information


tRNA (cytidine32/uridine32-2'-O)-methyltransferase / tRNA nucleoside ribose methylation / tRNA (uracil-2'-O-)-methyltransferase activity / RNA binding / cytosol
Similarity search - Function
RNA methyltransferase TrmJ/LasT / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJaroensuk, J. / Atichartpongkul, S. / Chionh, Y.H. / Wong, Y.H. / Liew, C.W. / McBee, M.E. / Thongdee, N. / Prestwich, E.G. / DeMott, M.S. / Mongkolsuk, S. ...Jaroensuk, J. / Atichartpongkul, S. / Chionh, Y.H. / Wong, Y.H. / Liew, C.W. / McBee, M.E. / Thongdee, N. / Prestwich, E.G. / DeMott, M.S. / Mongkolsuk, S. / Dedon, P.C. / Lescar, J. / Fuangthong, M.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa.
Authors: Jaroensuk, J. / Atichartpongkul, S. / Chionh, Y.H. / Wong, Y.H. / Liew, C.W. / McBee, M.E. / Thongdee, N. / Prestwich, E.G. / DeMott, M.S. / Mongkolsuk, S. / Dedon, P.C. / Lescar, J. / Fuangthong, M.
History
DepositionJul 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 2.0Dec 13, 2017Group: Database references / Derived calculations / Polymer sequence
Category: citation / entity_poly / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_poly.pdbx_target_identifier / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ
B: tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ
C: tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ
D: tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ


Theoretical massNumber of molelcules
Total (without water)75,6184
Polymers75,6184
Non-polymers00
Water11,331629
1
A: tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ
B: tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ


Theoretical massNumber of molelcules
Total (without water)37,8092
Polymers37,8092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-8 kcal/mol
Surface area14920 Å2
MethodPISA
2
C: tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ
D: tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ


Theoretical massNumber of molelcules
Total (without water)37,8092
Polymers37,8092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-7 kcal/mol
Surface area14810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.442, 65.043, 93.186
Angle α, β, γ (deg.)90.00, 110.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ / tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase / tRNA Cm32/Um32 methyltransferase


Mass: 18904.529 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 24-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: B136-33 / Gene: trmJ / Plasmid: pNIC-CH2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A072ZPM2, tRNA (cytidine32/uridine32-2'-O)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Bis-Tris pH 6.5, Ammonium chloride, PEG 3350

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Data collection

DiffractionMean temperature: 110 K / Ambient temp details: 110
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 29, 2014 / Details: toroidal focusing
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→24.89 Å / Num. obs: 75444 / % possible obs: 93.4 % / Redundancy: 2.8 % / Biso Wilson estimate: 23.22 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 12.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.5 / % possible all: 93.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CND

4cnd


Resolution: 1.7→24.27 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.104 / SU Rfree Blow DPI: 0.096 / SU Rfree Cruickshank DPI: 0.093
RfactorNum. reflection% reflectionSelection details
Rfree0.193 3782 5.01 %RANDOM
Rwork0.169 ---
obs0.17 75444 93.4 %-
Displacement parametersBiso mean: 27.46 Å2
Baniso -1Baniso -2Baniso -3
1--2.3661 Å20 Å24.9329 Å2
2--2.3392 Å20 Å2
3---0.0269 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: 1 / Resolution: 1.7→24.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5155 0 0 652 5807
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015340HARMONIC2
X-RAY DIFFRACTIONt_angle_deg17281HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1837SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes138HARMONIC2
X-RAY DIFFRACTIONt_gen_planes805HARMONIC5
X-RAY DIFFRACTIONt_it5340HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion15.92
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion695SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6782SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.74 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 259 4.97 %
Rwork0.224 4950 -
all0.226 5209 -
obs--87.62 %

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