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- PDB-3axt: Complex structure of tRNA methyltransferase Trm1 from Aquifex aeo... -

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Basic information

Entry
Database: PDB / ID: 3axt
TitleComplex structure of tRNA methyltransferase Trm1 from Aquifex aeolicus with S-adenosyl-L-Methionine
ComponentsProbable N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1
KeywordsTRANSFERASE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / tRNA modification enzyme / guanine 26 / N2 / N2-dimethyltransferase / Aquifex aeolicus
Function / homology
Function and homology information


tRNA (guanine26-N2/guanine27-N2)-dimethyltransferase / tRNA (guanine(26)-N2/guanine(27)-N2)-dimethyltransferase activity / tRNA N2-guanine methylation / tRNA (guanine(26)-N2)-dimethyltransferase activity / 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
S-ADENOSYLMETHIONINE / tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.491 Å
AuthorsIhsanawati / Sengoku, T. / Yokoyama, S. / Bessho, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Substrate tRNA recognition mechanism of a multisite-specific tRNA methyltransferase, Aquifex aeolicus Trm1, based on the X-ray crystal structure
Authors: Awai, T. / Ochi, A. / Ihsanawati / Sengoku, T. / Hirata, A. / Bessho, Y. / Yokoyama, S. / Hori, H.
History
DepositionApr 14, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3967
Polymers45,5481
Non-polymers8486
Water95553
1
A: Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1
hetero molecules

A: Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,79314
Polymers91,0962
Non-polymers1,69612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3070 Å2
ΔGint-14 kcal/mol
Surface area31080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.438, 140.928, 119.038
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-420-

HOH

21A-426-

HOH

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Components

#1: Protein Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1 / tRNA 2 / 2-dimethylguanosine-26 methyltransferase / tRNA(guanine-26 / N(2)-N(2)) methyltransferase ...tRNA 2 / 2-dimethylguanosine-26 methyltransferase / tRNA(guanine-26 / N(2)-N(2)) methyltransferase / tRNA(m(2 / 2)G26)dimethyltransferase


Mass: 45548.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: trm1 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O67010, EC: 2.1.1.32
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


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


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Na-Citrate, 2M (NH4)2SO4, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.491→30 Å / Num. obs: 16410 / % possible obs: 99.8 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.5→2.59 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EJT

2ejt


Resolution: 2.491→27.415 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.8659 / SU ML: 0.28 / σ(F): 1.36 / Phase error: 20.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 793 4.84 %RANDOM
Rwork0.1853 ---
obs0.1871 16387 99.74 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.241 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso max: 127.48 Å2 / Biso mean: 44.2779 Å2 / Biso min: 9.95 Å2
Baniso -1Baniso -2Baniso -3
1-2.9945 Å20 Å2-0 Å2
2--1.5296 Å2-0 Å2
3----4.5242 Å2
Refinement stepCycle: LAST / Resolution: 2.491→27.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 48 53 3263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023295
X-RAY DIFFRACTIONf_angle_d0.564439
X-RAY DIFFRACTIONf_chiral_restr0.039475
X-RAY DIFFRACTIONf_plane_restr0.002558
X-RAY DIFFRACTIONf_dihedral_angle_d10.9051263
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4908-2.64670.30821300.24242522265299
2.6467-2.85090.31941230.232825742697100
2.8509-3.13740.24761340.200725772711100
3.1374-3.59050.21241270.183225942721100
3.5905-4.52040.18451300.155626202750100
4.5204-27.41650.21351490.1827072856100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.10430.0902-0.10710.178-0.04030.12940.0783-0.0163-0.04930.17520.02220.05160.0397-0.13380.01050.2403-0.0988-0.06980.2570.17260.234112.744112.763449.4351
20.00960.0086-0.0060.006-0.00650.00580.0197-0.0181-0.03770.00530.03210.03020.0306-0.01620.02260.2806-0.1193-0.1937-0.05110.29980.144914.98650.574147.1417
30.1628-0.0230.08780.013-0.0370.17490.0424-0.046-0.00150.0262-0.00680.00570.0719-0.0004-0.04590.2491-0.0549-0.07530.23720.06250.241419.82814.078435.3603
40.1931-0.02840.02920.00770.00080.19390.1182-0.07860.05020.00160.06740.0501-0.0522-0.1308-0.01060.087-0.00450.00740.15470.03070.117520.227629.98740.1517
50.11110.1387-0.00290.5560.43470.53490.147-0.00290.09960.00810.20920.0498-0.292-0.0687-0.20260.31310.00420.06480.15070.01010.273820.49847.132336.0524
60.0822-0.0902-0.03450.27220.09770.0350.115-0.13130.0530.12380.07240.0379-0.0721-0.2274-0.0760.24990.02650.06510.3590.07860.20138.104134.795348.7915
70.06080.07990.11430.11110.16080.23650.1309-0.06280.0603-0.0517-0.06850.00810.01950.00890.01870.35760.08730.12290.3614-0.01790.24018.690752.567456.7062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:86)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 87:110)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 111:147)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 148:229)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 230:272)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 273:335)A0
7X-RAY DIFFRACTION7chain 'A' and (resseq 336:387)A0

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