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- PDB-2dul: Crystal structure of tRNA G26 methyltransferase Trm1 in apo form ... -

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Basic information

Entry
Database: PDB / ID: 2dul
TitleCrystal structure of tRNA G26 methyltransferase Trm1 in apo form from Pyrococcus horikoshii
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 N2-guanine methylation / tRNA (guanine(10)-N2)-methyltransferase activity / 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
tRNA (guanine(26)-N(2))-dimethyltransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, molecular replacement / Resolution: 1.9 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
DepositionJul 24, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)43,1032
Polymers43,0111
Non-polymers921
Water5,765320
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)86,2064
Polymers86,0222
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3710 Å2
ΔGint-21 kcal/mol
Surface area28260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.909, 109.662, 96.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsthere are one molecule in the asymmetric unit cell but the molecule have intensively contacts with the neighbouring molecule via 2 fold crystallographic axis. The exact function of the protein requires further experiment.

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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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES buffer, 2M NaCl, 14% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B211
SYNCHROTRONSPring-8 BL26B221.0718, 1.0712, 1.0539
Detector
TypeIDDetectorDate
RIGAKU JUPITER 2101CCDMay 18, 2006
RIGAKU JUPITER 2102CCDApr 24, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SiSINGLE WAVELENGTHMx-ray1
2SiMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.07181
31.07121
41.05391
ReflectionResolution: 1.9→50 Å / Num. obs: 31798 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.8 Å2 / Rsym value: 0.056 / Net I/σ(I): 35.09
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 5.09 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD, molecular replacement / Resolution: 1.9→48.34 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4066890.57 / 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
Rfree0.227 1578 5 %RANDOM
Rwork0.195 ---
obs0.195 31706 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.1843 Å2 / ksol: 0.36243 e/Å3
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.09 Å20 Å20 Å2
2---10.71 Å20 Å2
3---15.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 6 320 3264
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 260 5 %
Rwork0.249 4955 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3gol.paramgol.top

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