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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qok
TitleCrystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 14 (Methyl 2-aminopyridine-4-carboxylate)
ComponentstRNA (guanine-N(1)-)-methyltransferaseTRNA (guanine9-N1)-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 (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
methyl 2-azanylpyridine-4-carboxylate / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 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: Nucleic Acids Res. / Year: 2020
Title: Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification.
Authors: Thomas, S.E. / Whitehouse, A.J. / Brown, K. / Burbaud, S. / Belardinelli, J.M. / Sangen, J. / Lahiri, R. / Libardo, M.D.J. / Gupta, P. / Malhotra, S. / Boshoff, H.I.M. / Jackson, M. / Abell, ...Authors: Thomas, S.E. / Whitehouse, A.J. / Brown, K. / Burbaud, S. / Belardinelli, J.M. / Sangen, J. / Lahiri, R. / Libardo, M.D.J. / Gupta, P. / Malhotra, S. / Boshoff, H.I.M. / Jackson, M. / Abell, C. / Coyne, A.G. / Blundell, T.L. / Floto, R.A. / Mendes, V.
History
DepositionFeb 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 26, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)53,3666
Polymers52,8692
Non-polymers4964
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-32 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.702, 78.625, 86.484
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 / TRNA (guanine9-N1)-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-J9T / methyl 2-azanylpyridine-4-carboxylate


Mass: 152.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
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: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.48→86.48 Å / Num. obs: 85093 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 21.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.019 / Rrim(I) all: 0.053 / Net I/σ(I): 21.1 / Num. measured all: 646141 / Scaling rejects: 62
Reflection shell

Diffraction-ID: 1 / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.48-1.567.40.885122710.7450.3460.952
4.67-86.486.70.03329310.9990.0130.036

-
Phasing

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

-
Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHASER2.5.7phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→58.177 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.55
RfactorNum. reflection% reflection
Rfree0.1987 4248 5 %
Rwork0.17 --
obs0.1714 85011 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 292.23 Å2 / Biso mean: 30.3974 Å2 / Biso min: 12.19 Å2
Refinement stepCycle: final / Resolution: 1.48→58.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 32 334 3657
Biso mean--45.62 41.48 -
Num. residues----431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063441
X-RAY DIFFRACTIONf_angle_d1.0524716
X-RAY DIFFRACTIONf_chiral_restr0.042532
X-RAY DIFFRACTIONf_plane_restr0.006613
X-RAY DIFFRACTIONf_dihedral_angle_d12.61255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.4756-1.49240.33181300.301926532783
1.4924-1.50990.32281300.284526742804
1.5099-1.52830.29141410.267826262767
1.5283-1.54770.27031380.244726822820
1.5477-1.56810.31021510.23326842835
1.5681-1.58950.22441200.214326502770
1.5895-1.61230.23811420.205826522794
1.6123-1.63630.22791600.198626832843
1.6363-1.66190.21641520.193226402792
1.6619-1.68910.22711540.188626412795
1.6891-1.71830.25451470.189626612808
1.7183-1.74950.22421440.183926872831
1.7495-1.78320.21211370.178726502787
1.7832-1.81960.23081140.176327072821
1.8196-1.85910.2361090.171627132822
1.8591-1.90240.21481320.174526742806
1.9024-1.950.17751230.161527172840
1.95-2.00270.17911500.163226732823
2.0027-2.06160.18581470.168726922839
2.0616-2.12820.21371440.17126742818
2.1282-2.20420.19161420.16626752817
2.2042-2.29250.1971720.165526762848
2.2925-2.39680.20221470.166826972844
2.3968-2.52320.1771490.168326902839
2.5232-2.68130.20611460.177526972843
2.6813-2.88830.21641450.179927312876
2.8883-3.17890.20251290.173327502879
3.1789-3.63890.18481460.165727502896
3.6389-4.58430.14971500.138627632913
4.5843-58.2220.2091570.159329013058
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)
11.6597-0.4327-0.24431.13151.68253.18150.05860.5053-0.1579-0.4481-0.1752-0.0836-0.0024-0.12460.02980.21430.00620.01560.3019-0.00670.2098-32.335413.5221-22.327
20.00610.0033-0.01350.0170.00620.02110.00380.0066-0.1914-0.07690.00140.37350.125-0.13450.00010.526-0.0476-0.02610.5844-0.18510.6358-32.97551.1124-30.934
31.581-0.1397-0.07571.19050.50572.09680.04430.1630.2229-0.11950.0612-0.1061-0.2603-0.0556-0.06930.17790.01850.01710.20850.0260.206-36.525923.2957-10.3346
41.7696-0.5577-0.89750.61320.27581.4402-0.0442-0.003-0.1218-0.05370.02840.01810.0638-0.04260.05010.1615-0.01070.00640.1556-0.00330.1722-28.90189.4155-10.7143
51.3141-0.1228-0.67470.44650.11311.0131-0.02160.019-0.0694-0.01920.0236-0.03920.0209-0.02560.020.1595-0.0024-0.00250.1565-0.01020.1733-25.233311.2191-11.5693
61.60.889-0.82421.1974-0.31420.49980.07330.0729-0.1312-0.1643-0.22550.17090.1993-0.1881-0.19350.3856-0.0233-0.0380.3295-0.13510.34-19.4242-0.737-26.6589
71.3973-0.4235-0.57150.83410.59922.087-0.10950.079-0.0243-0.2814-0.0882-0.08420.3077-0.03040.00870.2453-0.03340.00250.1645-0.02220.14-1.84054.5119-36.355
80.9124-0.5195-0.22462.0582-0.53991.02520.04240.02380.1326-0.37220.1218-0.375-0.04870.19720.00180.2553-0.03160.03880.2189-0.01950.21934.71534.1599-41.2038
91.1823-0.6673-0.84482.42221.9071.9453-0.0148-0.18120.11360.13020.1462-0.32020.09170.1732-0.02470.20550.0295-0.03020.2357-0.01390.17393.01921.9825-24.151
101.9016-0.619-0.66261.2940.60381.44830.05620.180.0279-0.1506-0.1470.3967-0.2635-0.2611-0.07760.23750.0155-0.00690.23230.00470.2044-16.616817.9191-36.0047
111.1222-0.2571-0.78240.620.48491.49140.04980.01940.1248-0.14550.0241-0.048-0.13870.0229-0.10490.1817-0.01610.00880.1407-0.00610.1708-8.761919.66-26.937
121.9796-0.3184-0.69870.58370.28510.3882-0.1064-0.38460.26750.18590.1491-0.1740.0410.1325-0.05960.19890.0135-0.03220.2906-0.05910.2258-22.623119.63214.7023
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 18 )A0 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 29 )A19 - 29
3X-RAY DIFFRACTION3chain 'A' and (resid 30 through 62 )A30 - 62
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 115 )A63 - 115
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 155 )A116 - 155
6X-RAY DIFFRACTION6chain 'A' and (resid 156 through 178 )A156 - 178
7X-RAY DIFFRACTION7chain 'A' and (resid 179 through 188 )A179 - 188
8X-RAY DIFFRACTION8chain 'A' and (resid 189 through 203 )A189 - 203
9X-RAY DIFFRACTION9chain 'A' and (resid 204 through 227 )A204 - 227
10X-RAY DIFFRACTION10chain 'B' and (resid 0 through 62 )B0 - 62
11X-RAY DIFFRACTION11chain 'B' and (resid 63 through 181 )B63 - 181
12X-RAY DIFFRACTION12chain 'B' and (resid 182 through 231 )B182 - 231

+
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