[English] 日本語
Yorodumi
- PDB-6w15: Crystal structure of tRNA (guanine-N(1)-)-methyltransferase with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w15
TitleCrystal structure of tRNA (guanine-N(1)-)-methyltransferase with bound SAH from Mycobacterium smegmatis
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / SSGCID / tRNA (guanine-N(1)-)-methyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA N1-guanine methylation / cytosol
Similarity search - Function
tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase TrmD / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (guanine-N(1)-)-methyltransferase / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of tRNA (guanine-N(1)-)-methyltransferase with bound SAH from Mycobacterium smegmatis
Authors: Dranow, D.M. / Bolejack, M.J. / Abendroth, J.A. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMar 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 22, 2025Group: Data collection / Structure summary / Category: audit_author / chem_comp / pdbx_entry_details
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4422
Polymers26,0571
Non-polymers3841
Water1,08160
1
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules

A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8834
Polymers52,1152
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6700 Å2
ΔGint-8 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.100, 59.100, 114.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein tRNA (guanine-N(1)-)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase


Mass: 26057.330 Da / Num. of mol.: 1 / Fragment: MysmA.00937.a.AE1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: trmD, MSMEI_2377 / Plasmid: MysmA.00937.a.AE1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I7FBD0, UniProt: A0QV40*PLUS, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.92 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MysmA.00937.a.AE1.PW38670 at 19.05 mg/ml, incubated with 5 mM SAH, mixed 1:1 with MCSG1(a10): 28% (v/v) PPG P400, 0.1 M HEPES:NaOH, pH = 7.5, 0.2 M CaCl2. Tray: 311562a10. Puck: dcp5-10.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 14157 / % possible obs: 98.4 % / Redundancy: 24.126 % / Biso Wilson estimate: 44.465 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.038 / Χ2: 0.982 / Net I/σ(I): 55.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.0516.1590.6214.7610430.9870.64299.9
2.05-2.1117.8110.5026.2710050.9750.51699.8
2.11-2.1719.5510.4048.579660.9860.41599.4
2.17-2.2420.5420.30611.829410.9970.31498.9
2.24-2.3121.8250.24814.759100.9960.25497.4
2.31-2.3923.780.18220.158950.9980.18697.8
2.39-2.4826.3750.15325.398370.9990.15697
2.48-2.5827.8740.13229.578120.9990.13496.4
2.58-2.727.8510.10536.878110.9990.10798.3
2.7-2.8327.8230.08343.937410.9990.08497.4
2.83-2.9827.8810.05958.6372510.0697.4
2.98-3.1627.9010.04476.5669510.04599
3.16-3.3827.7020.03690.3365210.03797.6
3.38-3.6527.4810.028116.8261710.02899
3.65-427.2530.023139.7957010.02498.6
4-4.4726.7140.02150.9452110.0298.7
4.47-5.1626.6030.018159.9347310.01899.6
5.16-6.3225.8920.02156.6540810.0299.5
6.32-8.9424.6340.018159.3432810.019100
8.94-5020.4110.017161.1920710.01898.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZHI

5zhi


Resolution: 2→41.79 Å / SU ML: 0.2308 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4062
RfactorNum. reflection% reflection
Rfree0.2629 1373 9.71 %
Rwork0.203 --
obs0.2087 14147 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.38 Å2
Refinement stepCycle: LAST / Resolution: 2→41.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 26 60 1643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621620
X-RAY DIFFRACTIONf_angle_d0.80532211
X-RAY DIFFRACTIONf_chiral_restr0.0523249
X-RAY DIFFRACTIONf_plane_restr0.0045301
X-RAY DIFFRACTIONf_dihedral_angle_d18.0736603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.32331490.26751240X-RAY DIFFRACTION99.71
2.07-2.150.29751500.25481254X-RAY DIFFRACTION99.57
2.15-2.250.30971390.23521243X-RAY DIFFRACTION98.43
2.25-2.370.34391300.24411251X-RAY DIFFRACTION97.6
2.37-2.520.26881310.23651229X-RAY DIFFRACTION97.35
2.52-2.710.32661350.24861253X-RAY DIFFRACTION97.27
2.71-2.990.32781240.25171274X-RAY DIFFRACTION97.22
2.99-3.420.30141230.22271285X-RAY DIFFRACTION98.32
3.42-4.30.22771430.16481325X-RAY DIFFRACTION98.92
4.31-41.790.21351490.17261420X-RAY DIFFRACTION99.3
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)
18.7970822605-1.94382466497-6.410610527474.09535287441.916498755114.723898799630.108012084704-0.04168319323460.362934394379-0.1972539736380.2373898266170.00572815115351-0.9957982729210.503635099226-0.3643323424210.415629957967-0.0953516069469-0.06908644943990.392630008997-0.08536160509310.34369613999913.48793252238.754296289849.383108724
27.90214839523-5.21888111754-3.388568213975.51596686192.261203673122.6341161578-0.338876410309-0.6756739838670.3467118096350.2460053087520.529221457494-0.780899748023-0.1177369382380.761632179473-0.2494403555280.321966667967-0.0664891182019-0.06525894114830.494160252215-0.1635876020420.51719679129425.04535900892.006092635399.14185797969
33.2600401372-1.85697835627-1.438585066544.432477565032.272751149274.41131604252-0.193706457501-0.5378550413570.1217182118650.5442391857310.454812437598-0.4798718667770.5215439961480.662179557842-0.3633780667340.3872145614570.0473270685581-0.09249952816610.300950337496-0.05027565768780.36441789035819.3292327083-7.468420108559.8740182246
42.78017912351-1.22188950327-0.2477215832624.175362919791.805912250383.52441692049-0.146039938229-0.29250727368-0.06400080948870.4406847154330.286173304663-0.007014865018550.4533304849650.0736362100697-0.1498647561020.304028921371-0.0763512287232-0.001636487391610.2465023478630.009516096235380.2392811962147.27603793381-2.40490345559.62825071995
55.62613641627-0.313116478074.359345279970.0586022604285-0.1924506811773.52559066885-0.19751782953-0.0315688010315-0.1011723569350.3053491232910.3470051451520.101723533285-0.364585572373-0.266591871265-0.05828911804810.334534906596-0.07615723629630.06063669730420.425485380438-0.01686852190280.468670510509-13.35749810248.672155319753.84956420237
65.444852059463.01244765019-0.7809845481162.35500609961-1.351437299231.691755544720.8506839934471.025516121091.19178848723-0.557008340564-0.487085542350.497460872297-0.880290981343-0.14832317727-0.3856559424730.494753703170.2778264086890.05232665220840.8039173600520.1023879111550.521361467088-21.245147847421.6459933501-9.21367745219
77.97923892622-5.55605128823-0.838623766014.497241346650.8518441997541.13442564928-0.05265774612270.712791652027-0.9807288334590.14682003664-0.3951420816090.8522136284790.377700625006-0.6467913854910.4213035020560.469618295602-0.224775055051-0.004098442980630.775521406163-0.1891511164750.539474927754-20.98984844814.75719251503-2.56958788545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 155 )
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 180 )
6X-RAY DIFFRACTION6chain 'A' and (resid 181 through 200 )
7X-RAY DIFFRACTION7chain 'A' and (resid 201 through 225 )

+
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