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

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Basic information

Entry
Database: PDB / ID: 5gmb
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 (cytidine(32)/uridine(32)-2'-O)-methyltransferase activity / tRNA nucleoside ribose methylation / 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: 1.62 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 1.1Dec 13, 2017Group: Database references / Derived calculations / Category: citation / 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 / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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_special_symmetry
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


Theoretical massNumber of molelcules
Total (without water)18,5141
Polymers18,5141
Non-polymers00
Water3,117173
1
A: tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ

A: tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ


Theoretical massNumber of molelcules
Total (without water)37,0282
Polymers37,0282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2740 Å2
ΔGint-11 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.796, 59.796, 124.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-204-

HOH

21A-342-

HOH

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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: 18514.092 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: B136-33 / Gene: trmJ / Plasmid: pNIC28-Bsa4 / 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.: 173 / 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: 3 Å3/Da / Density % sol: 58.97 % / Description: solid cubic crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MgCl2, CaCl2, PEG MME 550, PEG 20000, MOPS/Na-HEPES pH7.5
Temp details: 293.15

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Data collection

DiffractionMean temperature: 110 K / Ambient temp details: 110
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2015 / Details: toroidal focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→30.03 Å / Num. obs: 29132 / % possible obs: 95.4 % / Redundancy: 9.9 % / Biso Wilson estimate: 18.25 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 3.9 / % possible all: 71.5

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Processing

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

4cnd


Resolution: 1.62→29.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.084 / SU Rfree Blow DPI: 0.083 / SU Rfree Cruickshank DPI: 0.078
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1403 5.1 %RANDOM
Rwork0.178 ---
obs0.179 27532 93.4 %-
Displacement parametersBiso mean: 20.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.061 Å20 Å20 Å2
2---0.061 Å20 Å2
3---0.122 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.62→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 0 0 166 1461
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011350HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.021838HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d469SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes34HARMONIC2
X-RAY DIFFRACTIONt_gen_planes203HARMONIC5
X-RAY DIFFRACTIONt_it1350HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.37
X-RAY DIFFRACTIONt_other_torsion15.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion175SEMIHARMONIC5
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_contact1744SEMIHARMONIC4
LS refinement shellResolution: 1.62→1.68 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.259 -5.46 %
Rwork0.242 1332 -
all0.243 1409 -
obs--46.74 %

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