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- PDB-5c1i: m1A58 tRNA methyltransferase mutant - D170A -

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Basic information

Entry
Database: PDB / ID: 5c1i
Titlem1A58 tRNA methyltransferase mutant - D170A
ComponentstRNA (adenine(58)-N(1))-methyltransferase TrmI
KeywordsTRANSFERASE / TrmI / m1A
Function / homology
Function and homology information


tRNA (adenine(58)-N1)-methyltransferase activity / tRNA (adenine58-N1)-methyltransferase / tRNA (m1A) methyltransferase complex / tRNA methylation / tRNA processing
Similarity search - Function
: / 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
tRNA (adenine(58)-N(1))-methyltransferase TrmI
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsPonchon, L. / Degut, C. / 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 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 24, 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

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Assembly

Deposited unit
A: tRNA (adenine(58)-N(1))-methyltransferase TrmI
B: tRNA (adenine(58)-N(1))-methyltransferase TrmI
C: tRNA (adenine(58)-N(1))-methyltransferase TrmI
D: tRNA (adenine(58)-N(1))-methyltransferase TrmI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,6787
Polymers112,3904
Non-polymers2883
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12390 Å2
ΔGint-86 kcal/mol
Surface area35000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.429, 110.429, 306.441
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 28097.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: trmI, TT_C0244 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8GBB2, tRNA (adenine58-N1)-methyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.4 M ammonium sulfate and 10%, isopropanol (v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→95.635 Å / Num. all: 21045 / Num. obs: 21045 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 84.046 Å2 / Rpim(I) all: 0.052 / Rrim(I) all: 0.136 / Rsym value: 0.125 / Net I/av σ(I): 5.381 / Net I/σ(I): 9.6 / Num. measured all: 135340
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
3.1-3.276.80.6861.12018629770.2820.6862.4100
3.27-3.476.50.4191.91836128440.1750.4193.7100
3.47-3.716.60.272.91747226630.1120.275.5100
3.71-46.50.1554.91607524860.0640.1558.3100
4-4.386.40.10671476923200.0440.10611.1100
4.38-4.96.40.0916.41358521100.0360.09114.2100
4.9-5.666.50.11851220418920.0470.11814100
5.66-6.936.40.134.61043916380.0540.1314.1100
6.93-9.86.10.03614.9787512970.0160.03620.2100
9.8-95.6355.30.02718.143748180.0130.02720.899.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.9 Å81.13 Å
Translation3.9 Å81.13 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.5.1phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2pwy

2pwy


Resolution: 3.1→51.94 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2686 --
Rwork0.2002 --
obs-20952 99.95 %
Displacement parametersBiso max: 154.6 Å2 / Biso mean: 74.0131 Å2 / Biso min: 29.55 Å2
Refinement stepCycle: LAST / Resolution: 3.1→51.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6950 0 15 22 6987

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