[English] 日本語
Yorodumi
- PDB-3axs: Complex structure of tRNA methyltransferase Trm1 from Aquifex aeo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3axs
TitleComplex structure of tRNA methyltransferase Trm1 from Aquifex aeolicus with sinefungin
ComponentsProbable N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1
KeywordsTRANSFERASE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Trm1 / Aquifex aeolicus / tRNA modification enzyme / NPPSFA / National Project on Protein Structural and Functional Analyses / tRNA
Function / homology
Function and homology information


tRNA (guanine26-N2/guanine27-N2)-dimethyltransferase / tRNA (guanine(26)-N2/guanine(27)-N2)-dimethyltransferase activity / 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
SINEFUNGIN / tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.162 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 13, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,4758
Polymers45,5481
Non-polymers9277
Water1,69394
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)92,95116
Polymers91,0962
Non-polymers1,85414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2990 Å2
ΔGint-16 kcal/mol
Surface area30740 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-457-

HOH

21A-461-

HOH

-
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-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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, 2.1M (NH4)2SO4, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 19, 2008
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.162→30.53 Å / Num. obs: 24738 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.6 Å2
Reflection shellResolution: 2.17→2.25 Å / % possible all: 99.8

-
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: PDB ENTRY 2YXA

2yxa
PDB Unreleased entry


Resolution: 2.162→30.53 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8505 / SU ML: 0.27 / σ(F): 1.35 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 1197 4.84 %RANDOM
Rwork0.1856 ---
obs0.1872 24710 99.1 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.901 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso max: 114.77 Å2 / Biso mean: 46.1606 Å2 / Biso min: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.398 Å20 Å2-0 Å2
2--9.2243 Å2-0 Å2
3----6.8263 Å2
Refinement stepCycle: LAST / Resolution: 2.162→30.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 53 94 3309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053290
X-RAY DIFFRACTIONf_angle_d0.8664431
X-RAY DIFFRACTIONf_chiral_restr0.055475
X-RAY DIFFRACTIONf_plane_restr0.003556
X-RAY DIFFRACTIONf_dihedral_angle_d13.3891256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1617-2.24820.24051220.21112375249792
2.2482-2.35050.27331260.206526022728100
2.3505-2.47440.25541340.207726182752100
2.4744-2.62930.27071390.202325892728100
2.6293-2.83220.3361200.202926252745100
2.8322-3.11690.23191420.208726142756100
3.1169-3.56740.23181320.19726552787100
3.5674-4.49220.17031290.157526742803100
4.4922-30.53280.19231530.176227612914100
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)
10.5936-0.1354-0.64151.04720.35760.81420.07250.1202-0.09590.1219-0.01530.11360.0422-0.1583-0.05250.2352-0.0565-0.01710.29260.12410.271212.818412.811549.4696
21.78810.9379-0.03040.56630.15471.13680.10620.1163-0.8765-0.19750.3948-0.08691.06190.1217-0.13260.4287-0.0835-0.0920.19270.17260.413615.05480.56847.0762
30.60280.3957-0.13960.83380.22610.63360.0103-0.1196-0.12540.01790.0494-0.00120.0097-0.1949-0.03620.14720.0031-0.01680.21890.03750.198719.835518.060537.3907
40.53370.16660.15730.463-0.03541.17550.14720.0365-0.09840.00780.238-0.0194-0.30690.0208-0.12010.18360.01040.06760.16280.0220.148624.730434.229239.4038
50.5409-0.0305-0.29940.09570.10810.48250.0939-0.0923-0.04880.0115-0.0185-0.0307-0.0278-0.3904-0.05230.19570.02630.01140.32120.08670.258413.868226.861640.0361
60.3992-0.3643-0.14820.86820.62382.92350.1582-0.02170.0853-0.27690.1202-0.0663-0.9614-0.1974-0.14810.43440.04830.08980.18310.02630.272820.576347.148936.1024
70.0907-0.2792-0.17181.59960.32151.22980.1139-0.0990.04930.20020.12550.2207-0.2796-0.3766-0.11320.25150.09670.08520.30170.06050.17618.308234.883948.9243
81.0617-0.3037-1.00160.7370.48110.83480.1281-0.2114-0.1341-0.12410.03640.2726-0.63920.0733-0.06260.50220.15840.11410.35740.030.28218.635446.929955.6355
90.6557-0.5431-0.38341.19821.33681.54040.24170.16930.4792-0.6021-0.32240.3999-0.2059-0.1095-0.03990.57910.24520.5360.148-0.25980.3339.308860.416958.4784
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 111:168)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 169:205)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 206:229)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 230:272)A0
7X-RAY DIFFRACTION7chain 'A' and (resseq 273:335)A0
8X-RAY DIFFRACTION8chain 'A' and (resseq 336:367)A0
9X-RAY DIFFRACTION9chain 'A' and (resseq 368:387)A0

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more