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- PDB-5c0o: m1A58 tRNA methyltransferase mutant - Y78A -

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Basic information

Entry
Database: PDB / ID: 5c0o
Titlem1A58 tRNA methyltransferase mutant - Y78A
ComponentstRNA (adenine(58)-N(1))-methyltransferase TrmI
KeywordsTRANSFERASE / TrmI / m1A
Function / homology
Function and homology information


tRNA (adenine58-N1)-methyltransferase / tRNA (m1A) methyltransferase complex / tRNA (adenine(58)-N1)-methyltransferase activity / tRNA methylation / tRNA processing
Similarity search - Function
TrmI-like N-terminal / tRNA (1-methyladenosine) methyltransferase catalytic subunit Gcd14 / : / tRNA methyltransferase complex GCD14 subunit / tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / tRNA (adenine(58)-N(1))-methyltransferase TrmI
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.62 Å
AuthorsDegut, C. / Ponchon, L. / Folly-Klan, M. / Barraud, P. / Tisne, C.
CitationJournal: Biophys.Chem. / Year: 2016
Title: The m1A58 modification in eubacterial tRNA: An overview of tRNA recognition and mechanism of catalysis by TrmI.
Authors: Degut, C. / Ponchon, L. / Folly-Klan, M. / Barraud, P. / Tisne, C.
History
DepositionJun 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
E: tRNA (adenine(58)-N(1))-methyltransferase TrmI
F: tRNA (adenine(58)-N(1))-methyltransferase TrmI
G: tRNA (adenine(58)-N(1))-methyltransferase TrmI
H: tRNA (adenine(58)-N(1))-methyltransferase TrmI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,8869
Polymers114,1964
Non-polymers1,6905
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12630 Å2
ΔGint-51 kcal/mol
Surface area35930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.540, 79.860, 184.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
tRNA (adenine(58)-N(1))-methyltransferase TrmI / tRNA(m1A58)-methyltransferase / tRNA(m1A58)MTase


Mass: 28549.006 Da / Num. of mol.: 4 / Mutation: Y78A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: trmI, TT_C0244 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8GBB2, tRNA (adenine58-N1)-methyltransferase
#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.1 M ammonium sulfate, 8% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.872 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2013
RadiationMonochromator: bent cylindrical mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.872 Å / Relative weight: 1
ReflectionResolution: 2.62→52.92 Å / Num. all: 34672 / Num. obs: 34672 / % possible obs: 99.88 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.354 Å2 / Rpim(I) all: 0.055 / Rrim(I) all: 0.104 / Rsym value: 0.089 / Net I/av σ(I): 6.559 / Net I/σ(I): 10.78 / Num. measured all: 139384
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.62-2.633.30.5391.41801255330.3460.539296
2.63-2.793.50.38121854853620.2370.3812.998.2
2.79-2.983.60.253.11820450980.1530.254.498.7
2.98-3.223.60.1465.11734648120.0890.1467.199.6
3.22-3.523.60.0997.31618444420.060.09910.499.8
3.52-3.943.60.06510.21470140560.0390.06514.599.9
3.94-4.553.60.05411.11289935820.0330.05417.599.8
4.55-5.573.50.05610.61070230740.0350.05618.399.6
5.57-7.883.40.068.8816124010.0380.0618.399.4
7.88-52.9233.30.04210.5462713920.0270.04221.798.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.02 Å52.92 Å
Translation7.02 Å52.92 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
SCALA3.3.21data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PWY

2pwy


Resolution: 2.62→52.923 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection
Rfree0.2824 -
Rwork0.2352 -
obs-34672
Displacement parametersBiso max: 141.57 Å2 / Biso mean: 41.1511 Å2 / Biso min: 6.27 Å2
Refinement stepCycle: LAST / Resolution: 2.62→52.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7019 0 113 132 7264

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