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- PDB-5e72: Crystal structure of the archaeal tRNA m2G/m22G10 methyltransfera... -

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Basic information

Entry
Database: PDB / ID: 5.0E+72
TitleCrystal structure of the archaeal tRNA m2G/m22G10 methyltransferase (aTrm11) in complex with S-adenosyl-L-methionine (SAM) from Thermococcus kodakarensis
ComponentsN2, N2-dimethylguanosine tRNA methyltransferase
KeywordsTRANSFERASE / tRNA methyltransferase / SAM
Function / homology
Function and homology information


tRNA (guanine) methyltransferase activity / : / tRNA methylation / RNA binding
Similarity search - Function
tRNA guanine(10)-N2-dimethyltransferase / Ribosomal RNA large subunit methyltransferase K/L-like, FLD domain / Putative RNA methylase family UPF0020 / THUMP / THUMP domain / THUMP domain / THUMP domain profile. / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / N2, N2-dimethylguanosine tRNA methyltransferase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.739 Å
AuthorsHirata, A.
Funding support Japan, 2items
OrganizationGrant numberCountry
KAKENHI15K06975 Japan
KAKENHI24770125 Japan
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structural and functional analyses of the archaeal tRNA m2G/m22G10 methyltransferase aTrm11 provide mechanistic insights into site specificity of a tRNA methyltransferase that contains common RNA-binding modules.
Authors: Hirata, A. / Nishiyama, S. / Tamura, T. / Yamauchi, A. / Hori, H.
History
DepositionOct 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N2, N2-dimethylguanosine tRNA methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6992
Polymers39,3001
Non-polymers3981
Water5,080282
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.602, 53.688, 134.787
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 N2, N2-dimethylguanosine tRNA methyltransferase


Mass: 39300.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0981 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q5JID5
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 4.5M NaCl, 0.1M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.739→50 Å / Num. obs: 36188 / % possible obs: 99.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 18.83 Å2 / Rmerge(I) obs: 0.043 / Χ2: 1.376 / Net I/av σ(I): 41.572 / Net I/σ(I): 16.9 / Num. measured all: 185983
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.74-1.85.10.21735291.12799.3
1.8-1.875.20.15935531.14499.6
1.87-1.965.20.12135741.19699.7
1.96-2.065.20.09136001.19399.8
2.06-2.195.30.06935441.23499.9
2.19-2.365.20.05836081.277100
2.36-2.65.20.04836211.297100
2.6-2.985.20.04636561.657100
2.98-3.754.90.04336642.55599.9
3.75-504.80.02338391.10798.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1682refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.739→32.674 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2231 1794 5 %
Rwork0.1868 34063 -
obs0.1887 35857 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.47 Å2 / Biso mean: 22.2948 Å2 / Biso min: 3.83 Å2
Refinement stepCycle: final / Resolution: 1.739→32.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2599 0 27 282 2908
Biso mean--21.05 29.51 -
Num. residues----323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072685
X-RAY DIFFRACTIONf_angle_d1.1013619
X-RAY DIFFRACTIONf_chiral_restr0.047387
X-RAY DIFFRACTIONf_plane_restr0.005468
X-RAY DIFFRACTIONf_dihedral_angle_d13.4411024
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.739-1.7860.26361300.21822611274199
1.786-1.83850.28791240.205126332757100
1.8385-1.89790.25231510.185825742725100
1.8979-1.96570.25871400.183726142754100
1.9657-2.04440.2211320.183126332765100
2.0444-2.13740.21321340.183126262760100
2.1374-2.25010.2251170.174826512768100
2.2501-2.3910.23651600.182426232783100
2.391-2.57550.23121250.20062619274499
2.5755-2.83460.25161250.21432667279299
2.8346-3.24440.24141470.20772613276098
3.2444-4.08640.2011570.16362591274896
4.0864-32.67950.18991520.17792608276092

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