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- PDB-2yx1: Crystal structure of M.jannaschii tRNA m1G37 methyltransferase -

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Basic information

Entry
Database: PDB / ID: 2yx1
TitleCrystal structure of M.jannaschii tRNA m1G37 methyltransferase
ComponentsHypothetical protein MJ0883Hypothesis
KeywordsTRANSFERASE / methyl transferase / trna modification enzyme
Function / homology
Function and homology information


tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA methylation / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #2580 / tRNA methyltransferase 5, N-terminal / tRNA methyltransferase 5 N-terminal domain / Met-10+ protein-like domains / SAM-dependent methyltransferase TRM5/TYW2-type domain profile. / SAM-dependent methyltransferase TRM5/TYW2-type / Met-10+ like-protein / GMP Synthetase; Chain A, domain 3 / Vaccinia Virus protein VP39 / Alpha-Beta Plaits ...Alpha-Beta Plaits - #2580 / tRNA methyltransferase 5, N-terminal / tRNA methyltransferase 5 N-terminal domain / Met-10+ protein-like domains / SAM-dependent methyltransferase TRM5/TYW2-type domain profile. / SAM-dependent methyltransferase TRM5/TYW2-type / Met-10+ like-protein / GMP Synthetase; Chain A, domain 3 / Vaccinia Virus protein VP39 / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SINEFUNGIN / tRNA (guanine(37)-N1)-methyltransferase Trm5b
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsGoto-Ito, S. / Ito, T. / Ishii, R. / Bessho, Y. / Yokoyama, S.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5.
Authors: Goto-Ito, S. / Ito, T. / Ishii, R. / Muto, Y. / Bessho, Y. / Yokoyama, S.
History
DepositionApr 23, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein MJ0883
B: Hypothetical protein MJ0883
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,93614
Polymers78,5192
Non-polymers1,41712
Water4,558253
1
A: Hypothetical protein MJ0883
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9036
Polymers39,2601
Non-polymers6435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein MJ0883
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0338
Polymers39,2601
Non-polymers7747
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Hypothetical protein MJ0883
hetero molecules

B: Hypothetical protein MJ0883
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,93614
Polymers78,5192
Non-polymers1,41712
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation2_656-x+1,y+1/2,-z+11
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-233.4 kcal/mol
Surface area31850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.000, 69.790, 87.150
Angle α, β, γ (deg.)90.00, 96.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hypothetical protein MJ0883 / Hypothesis / methyl transferase


Mass: 39259.527 Da / Num. of mol.: 2 / Fragment: 2.1.1.31
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pET28c / Production host: Escherichia coli (E. coli) / References: UniProt: Q58293
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M sodium cacodylate, 7.5% PEG 3350, 5% PEGMME 550, 0.02M Hepes pH 7.50, 0.002M zinc sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97934, 0.97942, 0.96418
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 5, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.979421
30.964181
ReflectionResolution: 2.2→50 Å / Num. obs: 36694 / % possible obs: 96.8 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.105 / Net I/σ(I): 21.9
Reflection shellResolution: 2.2→2.24 Å / % possible obs: 72.6 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 1.8 / % possible all: 72.6

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 2.2→47.9 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1279276.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1840 5 %RANDOM
Rwork0.224 ---
obs0.224 36563 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.6419 Å2 / ksol: 0.337142 e/Å3
Displacement parametersBiso mean: 46.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.44 Å20 Å22.89 Å2
2---7.38 Å20 Å2
3---3.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5168 0 64 253 5485
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.411.5
X-RAY DIFFRACTIONc_mcangle_it5.652
X-RAY DIFFRACTIONc_scbond_it6.542
X-RAY DIFFRACTIONc_scangle_it8.092.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 260 5 %
Rwork0.286 4902 -
obs--82.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3sfg_C2-endo.paramsfg_C2-endo.top
X-RAY DIFFRACTION4ion.paramion.top

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