[English] 日本語
Yorodumi
- PDB-6qr0: Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qr0
TitleCrystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / TrmD / tRNA methyltransferase / SPOUT methyltransferase
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA modification / methylation / cytoplasm
Similarity search - Function
tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases ...tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-JFB / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 Å
AuthorsThomas, S.E. / Whitehouse, A.J. / Coyne, A.G. / Abell, C. / Mendes, V. / Blundell, T.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privateCystic Fibrosis Trust Registered Charity No. (England and Wales) 1079049, Registered Charity No. (Scotland) SC040196 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2019
Title: Development of Inhibitors against Mycobacterium abscessus tRNA (m1G37) Methyltransferase (TrmD) Using Fragment-Based Approaches.
Authors: Whitehouse, A.J. / Thomas, S.E. / Brown, K.P. / Fanourakis, A. / Chan, D.S. / Libardo, M.D.J. / Mendes, V. / Boshoff, H.I.M. / Floto, R.A. / Abell, C. / Blundell, T.L. / Coyne, A.G.
History
DepositionFeb 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,5945
Polymers52,8692
Non-polymers7253
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-22 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.920, 77.170, 87.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 26434.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Gene: trmD, MAB_3226c / Production host: Escherichia coli (E. coli)
References: UniProt: B1MDI3, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-JFB / 5-azanyl-3-[1-(pyridin-4-ylmethyl)indol-6-yl]-1~{H}-pyrazole-4-carbonitrile


Mass: 314.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H14N6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.08M Sodium cacodylate pH 6.5 -7.0, 1-2 M Ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.59→56.81 Å / Num. obs: 68585 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 27.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.019 / Rrim(I) all: 0.058 / Net I/σ(I): 19 / Num. measured all: 603250 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.59-1.6391.58149980.5740.5491.677100
7.11-56.817.50.0438770.9980.0170.04699.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

-
Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHASER2.5.7phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NVR

6nvr


Resolution: 1.59→56.81 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.29
RfactorNum. reflection% reflection
Rfree0.1987 3368 4.92 %
Rwork0.1737 --
obs0.175 68509 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.31 Å2 / Biso mean: 34.634 Å2 / Biso min: 19.21 Å2
Refinement stepCycle: final / Resolution: 1.59→56.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 53 302 3525
Biso mean--27.02 44.58 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063338
X-RAY DIFFRACTIONf_angle_d1.0524577
X-RAY DIFFRACTIONf_chiral_restr0.043513
X-RAY DIFFRACTIONf_plane_restr0.006590
X-RAY DIFFRACTIONf_dihedral_angle_d12.8781201
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.59-1.61270.31481400.289426632803
1.6127-1.63680.26011530.2826742827
1.6368-1.66240.25561430.257426862829
1.6624-1.68960.27381270.243426852812
1.6896-1.71880.26581410.235726742815
1.7188-1.750.2491500.22526782828
1.75-1.78370.23181390.20826732812
1.7837-1.82010.21571300.192327102840
1.8201-1.85970.22791280.19127032831
1.8597-1.90290.24881280.183426892817
1.9029-1.95050.2121470.185727002847
1.9505-2.00330.21481210.174226992820
2.0033-2.06220.18511250.177927142839
2.0622-2.12880.24391290.173827332862
2.1288-2.20490.19461330.175827072840
2.2049-2.29320.21011560.162926822838
2.2932-2.39750.16811480.166227162864
2.3975-2.52390.16411360.169927072843
2.5239-2.68210.25061280.184727462874
2.6821-2.88910.20621410.192127372878
2.8891-3.17990.21411550.186627222877
3.1799-3.63990.19911540.166727612915
3.6399-4.58560.18331770.143127572934
4.5856-56.84890.16231390.161529253064
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)
10.0665-0.03110.04950.039-0.05440.06940.06910.3923-0.0896-0.4239-0.18790.04890.1293-0.20780.00020.34460.00830.00030.33080.00850.2561-32.063513.0007-22.5212
20.5749-0.0117-0.23270.197-0.25240.42530.06740.15430.0761-0.22530.10990.0157-0.227-0.04540.00010.26450.0098-0.01910.2811-0.00480.3004-36.512118.6122-14.2544
30.6858-0.0377-0.10050.18-0.03430.49-0.0202-0.01280.0245-0.0270.05240.02250.0604-0.0184-00.2277-0.0147-0.00610.2216-0.01340.2324-28.073710.043-11.1683
40.00630.0013-0.0076-0.0024-0.00550.00710.090.2844-0.1348-0.1522-0.27180.26360.1951-0.012-0.00010.5368-0.0217-0.05350.4232-0.13570.372-19.8709-0.5944-27.0096
50.0783-0.04510.01370.09890.02450.01760.00170.10190.0923-0.24250.1553-0.2444-0.07230.14420.00020.3278-0.04280.04510.3023-0.02630.28431.52654.8427-39.4641
60.13370.094-0.09280.0685-0.03190.0484-0.0567-0.07160.15820.23910.0741-0.22770.23270.26670.00010.290.0411-0.04450.3579-0.04680.28682.7042.096-24.3066
70.1681-0.09830.03260.1072-0.05480.06730.07590.26080.2980.0487-0.00870.4853-0.1499-0.3639-0.00020.38510.0057-0.03010.3710.05880.3492-18.303922.8501-34.4743
80.0467-0.0122-0.01040.03010.03570.0277-0.13370.0164-0.1373-0.01360.08620.3047-0.0208-0.0125-0.00030.3154-0.01590.02170.28470.00190.2644-8.96653.7156-40.9036
90.5382-0.221-0.24150.11190.11720.30660.00360.03470.0899-0.18860.0389-0.0826-0.1970.0384-0.00010.3227-0.04470.02180.24160.00160.2645-7.987120.3054-29.6844
100.007-0.02380.00790.0307-0.01120.00820.0125-0.04290.0407-0.15050.1525-0.1241-0.05750.35030.00050.3059-0.0920.03920.2937-0.02040.306-0.615618.6294-32.9508
110.1340.0363-0.06290.0652-0.09140.0924-0.01240.10940.1041-0.053-0.0316-0.0119-0.0164-0.1041-00.2375-0.0112-0.0030.2396-0.00430.2586-16.038917.0934-22.0302
120.03190.029-0.00040.08190.02360.0302-0.1151-0.08980.1047-0.13650.0392-0.1237-0.23930.0693-0.00060.3232-0.0415-0.03150.3227-0.02190.4416-16.547825.3309-7.2879
130.1007-0.0645-0.07280.03740.02240.06790.0564-0.37440.2660.21190.00620.15820.23190.0179-0.00010.27890.02280.02680.3544-0.06420.2958-33.511622.28376.4071
140.0818-0.0242-0.17240.01020.05350.3031-0.0151-0.49450.23030.2686-0.0226-0.12130.14-0.0728-0.00620.26630.0104-0.06090.5612-0.09170.3546-18.405519.2086.2166
150.0448-0.0188-0.01930.0119-0.0040.02090.07280.205-0.2186-0.0950.0442-0.15720.1811-0.19-0.00010.3062-0.0272-0.05530.3319-0.03180.4049-8.31388.8886-1.8462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 19 )A0 - 19
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 62 )A20 - 62
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 155 )A63 - 155
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 178 )A156 - 178
5X-RAY DIFFRACTION5chain 'A' and (resid 179 through 203 )A179 - 203
6X-RAY DIFFRACTION6chain 'A' and (resid 204 through 227 )A204 - 227
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 40 )B0 - 40
8X-RAY DIFFRACTION8chain 'B' and (resid 41 through 62 )B41 - 62
9X-RAY DIFFRACTION9chain 'B' and (resid 63 through 115 )B63 - 115
10X-RAY DIFFRACTION10chain 'B' and (resid 116 through 131 )B116 - 131
11X-RAY DIFFRACTION11chain 'B' and (resid 132 through 155 )B132 - 155
12X-RAY DIFFRACTION12chain 'B' and (resid 156 through 182 )B156 - 182
13X-RAY DIFFRACTION13chain 'B' and (resid 183 through 203 )B183 - 203
14X-RAY DIFFRACTION14chain 'B' and (resid 204 through 222 )B204 - 222
15X-RAY DIFFRACTION15chain 'B' and (resid 223 through 233 )B223 - 233

+
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