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- PDB-6emt: Crystal Structure of dual specific Trm10 construct from Thermococ... -

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Basic information

Entry
Database: PDB / ID: 6emt
TitleCrystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis.
ComponentstRNA (guanine(9)-/adenine(9)-N1)-methyltransferase
KeywordsRNA BINDING PROTEIN / Trm10 / Dual specificity enzymes / SPOUT / MTases
Function / homology
Function and homology information


tRNA (adenine(9)-N1)-methyltransferase activity / tRNA (adenine9-N1)-methyltransferase / tRNA (guanine9-N1)-methyltransferase / tRNA (guanosine(9)-N1)-methyltransferase activity / tRNA methylation / tRNA processing / cytoplasm
Similarity search - Function
tRNA methyltransferase, archaea / tRNA methyltransferase TRM10-type domain / tRNA methyltransferase TRM10-type domain superfamily / SAM-dependent methyltransferase TRM10-type domain profile.
Similarity search - Domain/homology
ACETATE ION / tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.794 Å
AuthorsSingh, R.K. / Versees, W.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds voor Wetenschappelijk Onderzoek (FWO) Belgium
CitationJournal: RNA / Year: 2018
Title: Structural and biochemical analysis of the dual-specificity Trm10 enzyme fromThermococcus kodakaraensisprompts reconsideration of its catalytic mechanism.
Authors: Singh, R.K. / Feller, A. / Roovers, M. / Van Elder, D. / Wauters, L. / Droogmans, L. / Versees, W.
History
DepositionOct 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,20112
Polymers22,4231
Non-polymers77911
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-1 kcal/mol
Surface area9160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.262, 62.262, 203.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

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Components

#1: Protein tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase / tRNA(m1G9/m1A9)-methyltransferase / tRNA(m1G9/m1A9)MTase


Mass: 22422.598 Da / Num. of mol.: 1 / Mutation: C120A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: TK0422 / Plasmid: Pet 28b
Details (production host): bacterial expression with T7lac promoter
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: Q5JD38, tRNA (adenine9-N1)-methyltransferase, tRNA (guanine9-N1)-methyltransferase
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5 / Details: 20 % PEG 3350, 8% v/v Tascimate / PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.794→47.645 Å / Num. obs: 22813 / % possible obs: 99.8 % / Redundancy: 37.9 % / Biso Wilson estimate: 34.5407666018 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09092 / Rpim(I) all: 0.0149 / Rrim(I) all: 0.092179 / Net I/σ(I): 30.85
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 36.5 % / Rmerge(I) obs: 2.361 / Mean I/σ(I) obs: 1.63 / Num. unique obs: 2160 / CC1/2: 0.763 / Rpim(I) all: 0.3871 / Rrim(I) all: 2.394 / % possible all: 97.87

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDS2015-10-15data reduction
XDS2015-10-15data scaling
PHASER2.5.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SPOUT domain of PDB ID 6EMS

6ems


Resolution: 1.794→47.645 Å / SU ML: 0.211230852015 / Cross valid method: THROUGHOUT / σ(F): 1.3634 / Phase error: 20.7317183315
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 1140 4.99846538343 %RANDOM
Rwork0.1914 ---
obs0.1921 22807 99.7637898605 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.0339235129 Å2
Refinement stepCycle: LAST / Resolution: 1.794→47.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1347 0 52 113 1512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003006629971191423
X-RAY DIFFRACTIONf_angle_d0.5154176343521907
X-RAY DIFFRACTIONf_chiral_restr0.0444691270129202
X-RAY DIFFRACTIONf_plane_restr0.00236177992714245
X-RAY DIFFRACTIONf_dihedral_angle_d13.5365816251834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.794-1.87570.3015415403781350.3115467807822585X-RAY DIFFRACTION98.1949458484
1.8757-1.97460.2888492457341380.2476087403372628X-RAY DIFFRACTION99.9277456647
1.9746-2.09830.2463180308371400.2162219356132658X-RAY DIFFRACTION100
2.0983-2.26030.2126917982561410.216503101072675X-RAY DIFFRACTION100
2.2603-2.48770.2145877216921410.2000804519952682X-RAY DIFFRACTION99.9645892351
2.4877-2.84770.2318718024371440.2065771246452725X-RAY DIFFRACTION100
2.8477-3.58760.1963138347011440.1810108432112746X-RAY DIFFRACTION100
3.5876-47.66130.1837040767721570.1713388833122968X-RAY DIFFRACTION100
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)
15.84355248786-1.145436082232.529886800572.34214363047-1.717161945845.12609663106-0.324250378772-0.702437378660.3210359118740.1990865684780.3202841504050.4348127130030.389057188922-0.567704975261-0.1048074323790.3432130080310.0970313372275-0.03583328875950.371490170016-0.04850141583380.343607825556-8.01861809717-23.25411518915.3542973666
25.51013848090.804960944392-2.480462505763.38623476426-2.246409856166.1570125444-0.1883308618640.1851331543630.0548193250596-0.3199306190520.031797749551-0.1272651278450.3165233938570.1862826785950.1651534486740.2169803391720.024431443392-0.05917275986430.178144733143-0.02553998088110.2294928037582.92193931799-28.02316106388.37214356051
33.10918903294-1.84717095163-1.507905562554.33429838005-2.488560102189.12847806826-0.159336635450.102934540784-0.1809335222-0.6019300873390.153930198520.2760296914270.519537777482-0.3541652634310.2545144710940.274918029938-0.0457543237915-0.09150643674720.281060690835-0.03724034450580.287637097933-4.65472915571-29.5727424045.89706933273
45.59673035463-1.821389501962.506988173477.05597422644-1.104133028434.79485872946-0.105946468349-0.0361667090840.0960812100246-0.1985365001550.009771399516280.368323498893-0.173630066451-0.4099463158660.04166186894720.2336369035930.023094730334-0.05272472472450.2355604505240.01748967295390.215944461936-9.45812718601-23.85524836128.06584197345
53.940538028474.44642277941-2.259129420698.00670087142-0.1198333926083.50285446669-0.00386793848062-0.2127997797131.228302784550.163816683696-0.2045002146520.426460027452-1.25754518701-0.4105715306610.0732821781520.6120283294390.095898609637-0.1905656044290.462777115708-0.05286998326090.454467657168-1.8541612725-11.157603328820.6224930595
62.84263724393-3.778694581332.234378663585.78088470379-1.259161372265.61273283543-0.07779899550050.01993915034060.604353563649-0.294839071431-0.265122919491-0.527918954051-1.015844411290.1956066932960.3794179581670.4212387066320.0152873542682-0.1065216748360.2575778782490.02539586516670.3404696713570.462857198776-15.99078795338.92789453541
73.572968819270.6526294394652.942625116672.375923618050.5695111545765.91615248699-0.268329362640.05106989508630.659286077774-0.273538520047-0.0214004594815-0.204283189332-0.8672771597460.1822982460410.2563296565670.4165456266870.00370069605174-0.1127447831040.196541824946-0.01019596425410.4183907617571.96534166974-15.463728616917.0305964575
82.19271201824-0.09108809933512.123195921623.71569603672-0.9132002869022.92525462988-0.081815919995-0.2704747530470.142903571142-0.07027053326560.103585772489-0.01219299559570.506616480725-0.2019308626510.004246937203230.4128896147820.00953783953499-0.108687261950.431020328452-0.1044817639240.343025613125.65014339874-21.32549209429.2164515823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 97 through 104 )
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 133 )
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 151 )
4X-RAY DIFFRACTION4chain 'A' and (resid 152 through 181 )
5X-RAY DIFFRACTION5chain 'A' and (resid 182 through 197 )
6X-RAY DIFFRACTION6chain 'A' and (resid 198 through 217 )
7X-RAY DIFFRACTION7chain 'A' and (resid 218 through 258 )
8X-RAY DIFFRACTION8chain 'A' and (resid 259 through 272 )

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