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- PDB-7edc: Crystal structure of mutant tRNA [Gm18] methyltransferase TrmH (E... -

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Basic information

Entry
Database: PDB / ID: 7edc
TitleCrystal structure of mutant tRNA [Gm18] methyltransferase TrmH (E107G) in complex with S-adenosyl-L-methionine from Escherichia coli
ComponentstRNA (guanosine(18)-2'-O)-methyltransferase
KeywordsTRANSFERASE / tRNA modification / 2-O' methylation / TrmH / Escherichia coli
Function / homology
Function and homology information


tRNA guanine ribose methylation / tRNA (guanosine18-2'-O)-methyltransferase / tRNA (guanine(18)-2'-O)-methyltransferase activity / tRNA binding
Similarity search - Function
RNA methyltransferase, SpoU/TrmH type, C-terminal / tRNA (guanosine(18)-2'-O)-methyltransferase / SpoU, rRNA methylase, C-terminal / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
PHOSPHATE ION / S-ADENOSYLMETHIONINE / tRNA (guanosine(18)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.946 Å
AuthorsKono, Y. / Ito, A. / Okamoto, A. / Yamagami, R. / Hirata, A. / Hori, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K06088 Japan
Japan Society for the Promotion of Science (JSPS)20H03211 Japan
CitationJournal: To Be Published
Title: Unique substrate specificity of type II tRNA Gm18 methyltransferase from Escherichia coli
Authors: Kono, Y. / Ito, A. / Okamoto, A. / Yamagami, R. / Hirata, A. / Hori, H.
History
DepositionMar 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Derived calculations / Category: atom_type / chem_comp_atom / chem_comp_bond / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA (guanosine(18)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9663
Polymers27,4721
Non-polymers4932
Water1,18966
1
A: tRNA (guanosine(18)-2'-O)-methyltransferase
hetero molecules

A: tRNA (guanosine(18)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9326
Polymers54,9452
Non-polymers9874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3020 Å2
ΔGint-14 kcal/mol
Surface area21140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.791, 60.942, 67.906
Angle α, β, γ (deg.)90.000, 122.965, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein tRNA (guanosine(18)-2'-O)-methyltransferase / tRNA [Gm18] methyltransferase


Mass: 27472.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trmH / Production host: Escherichia coli (E. coli)
References: UniProt: C3SM77, tRNA (guanosine18-2'-O)-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: PEG6000, HEPES, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.946→50 Å / Num. obs: 21319 / % possible obs: 99.9 % / Redundancy: 3.7 % / CC1/2: 0.96 / Rmerge(I) obs: 0.044 / Net I/σ(I): 41.9
Reflection shellResolution: 1.95→1.98 Å / Num. unique obs: 1060 / CC1/2: 0.734 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.946→30.977 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.066 / SU ML: 0.115 / Cross valid method: FREE R-VALUE / ESU R: 0.158 / ESU R Free: 0.148
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2421 1110 5.207 %
Rwork0.2024 20209 -
all0.204 --
obs-21319 99.436 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.254 Å2
Baniso -1Baniso -2Baniso -3
1--0.004 Å20 Å2-0.004 Å2
2--0.006 Å20 Å2
3---0.002 Å2
Refinement stepCycle: LAST / Resolution: 1.946→30.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 32 66 1918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131899
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171819
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.6392582
X-RAY DIFFRACTIONr_angle_other_deg1.3361.5774169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9035239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69121.5100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.9415320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0411516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022171
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02436
X-RAY DIFFRACTIONr_nbd_refined0.220.2408
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.21828
X-RAY DIFFRACTIONr_nbtor_refined0.1580.2882
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2944
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0210.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1570.216
X-RAY DIFFRACTIONr_nbd_other0.2370.2112
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.26
X-RAY DIFFRACTIONr_mcbond_it4.1594.465950
X-RAY DIFFRACTIONr_mcbond_other4.0884.466950
X-RAY DIFFRACTIONr_mcangle_it5.1926.6771185
X-RAY DIFFRACTIONr_mcangle_other5.1916.6811186
X-RAY DIFFRACTIONr_scbond_it5.2085.105948
X-RAY DIFFRACTIONr_scbond_other5.1335.102944
X-RAY DIFFRACTIONr_scangle_it7.3317.451395
X-RAY DIFFRACTIONr_scangle_other7.297.4461390
X-RAY DIFFRACTIONr_lrange_it9.03854.0212085
X-RAY DIFFRACTIONr_lrange_other9.04854.0032080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.946-1.9960.306800.2871462X-RAY DIFFRACTION97.9048
1.996-2.0510.312790.2591450X-RAY DIFFRACTION100
2.051-2.110.264900.2481389X-RAY DIFFRACTION99.865
2.11-2.1750.271750.2251411X-RAY DIFFRACTION99.9327
2.175-2.2460.287850.2161296X-RAY DIFFRACTION100
2.246-2.3250.28650.2221299X-RAY DIFFRACTION99.9267
2.325-2.4130.329590.2151248X-RAY DIFFRACTION99.9235
2.413-2.5110.252580.211217X-RAY DIFFRACTION99.9216
2.511-2.6220.226640.1941141X-RAY DIFFRACTION100
2.622-2.750.248590.1941114X-RAY DIFFRACTION99.9148
2.75-2.8980.225530.2081042X-RAY DIFFRACTION100
2.898-3.0730.254670.21991X-RAY DIFFRACTION100
3.073-3.2840.225520.216921X-RAY DIFFRACTION99.8973
3.284-3.5450.278440.205874X-RAY DIFFRACTION99.7826
3.545-3.8820.23480.199792X-RAY DIFFRACTION100
3.882-4.3360.183450.171742X-RAY DIFFRACTION99.7465
4.336-4.9990.216240.162641X-RAY DIFFRACTION99.8499
4.999-6.1050.258260.209560X-RAY DIFFRACTION100
6.105-8.560.273310.195427X-RAY DIFFRACTION98.9201
8.56-30.9770.1460.244192X-RAY DIFFRACTION74.1573

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