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- PDB-2eju: Complex structure of Trm1 from Pyrococcus horikoshii with S-adeno... -

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Basic information

Entry
Database: PDB / ID: 2eju
TitleComplex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-Homocystein
ComponentsN(2),N(2)-dimethylguanosine tRNA methyltransferase
KeywordsTRANSFERASE / tRNA modification enzyme / guanine-26 / N(2)-N(2)-dimethyltransferase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


tRNA (guanine26-N2)-dimethyltransferase / tRNA (guanine(26)-N2)-dimethyltransferase activity / tRNA (guanine(10)-N2)-methyltransferase activity / tRNA methylation / tRNA binding
Similarity search - Function
N2,N2-dimethylguanosine tRNA methyltransferase, C-terminal domain / tRNA (guanine(26)-N(2))-dimethyltransferase, archaeal and bacterial / tRNA methyltransferase, Trm1 / tRNA methyltransferase, Trm1, C-terminal / N2,N2-dimethylguanosine tRNA methyltransferase / Trm1 methyltransferase domain profile. / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold ...N2,N2-dimethylguanosine tRNA methyltransferase, C-terminal domain / tRNA (guanine(26)-N(2))-dimethyltransferase, archaeal and bacterial / tRNA methyltransferase, Trm1 / tRNA methyltransferase, Trm1, C-terminal / N2,N2-dimethylguanosine tRNA methyltransferase / Trm1 methyltransferase domain profile. / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (guanine(26)-N(2))-dimethyltransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsIhsanawati / Shirouzu, M. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal Structure of tRNA N(2),N(2)-Guanosine Dimethyltransferase Trm1 from Pyrococcus horikoshii
Authors: Ihsanawati / Nishimoto, M. / Higashijima, K. / Shirouzu, M. / Grosjean, H. / Bessho, Y. / Yokoyama, S.
History
DepositionMar 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N(2),N(2)-dimethylguanosine tRNA methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4873
Polymers43,0111
Non-polymers4772
Water6,053336
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: N(2),N(2)-dimethylguanosine tRNA methyltransferase
hetero molecules

A: N(2),N(2)-dimethylguanosine tRNA methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9756
Polymers86,0222
Non-polymers9534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3740 Å2
ΔGint-20 kcal/mol
Surface area28790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.781, 109.655, 96.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-868-

HOH

21A-904-

HOH

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Components

#1: Protein N(2),N(2)-dimethylguanosine tRNA methyltransferase / tRNA(guanine-26 / N(2)-N(2))methyltransferase / tRNA 2 / 2-dimethylguanosine-26 methyltransferase / ...tRNA(guanine-26 / N(2)-N(2))methyltransferase / tRNA 2 / 2-dimethylguanosine-26 methyltransferase / tRNA(m(2 / 2)G26)dimethyltransferase


Mass: 43010.938 Da / Num. of mol.: 1 / Fragment: residues 1-378 / Mutation: L1M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: trm1 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: O59493, EC: 2.1.1.32
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE RESIDUE WAS ENGINEERED FROM LEU TO MET AS INITIATING METHIONINE.

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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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES buffer, 2M NaCl, 15% PEG 6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 8, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 29246 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.1 Å2 / Rsym value: 0.061 / Net I/σ(I): 29.71
Reflection shellResolution: 1.95→2.02 Å / Mean I/σ(I) obs: 3.63 / Rsym value: 0.359 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DUL

2dul


Resolution: 1.95→48.26 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4174537.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1432 4.9 %RANDOM
Rwork0.2 ---
obs0.2 29208 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.4023 Å2 / ksol: 0.360094 e/Å3
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1--6.88 Å20 Å20 Å2
2---12.91 Å20 Å2
3---19.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 1.95→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2966 0 32 336 3334
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 224 4.7 %
Rwork0.31 4536 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3gol.paramgol.top
X-RAY DIFFRACTION4sah.paramsah.top

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