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

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Basic information

Entry
Database: PDB / ID: 6emu
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
S-ADENOSYLMETHIONINE / tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29745444787 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 1.2May 1, 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

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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
B: tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase
C: tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6478
Polymers67,2683
Non-polymers1,3795
Water1,40578
1
A: tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9133
Polymers22,4231
Non-polymers4912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8212
Polymers22,4231
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9133
Polymers22,4231
Non-polymers4912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.084, 71.084, 191.958
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61

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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.: 3 / Mutation: C120A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: TK0422 / Plasmid: pet28b
Details (production host): bacterial expression vector 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-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 10% PEG6000, 0.2M LiCl and 0.1M NaAc pH 5.5 / PH range: 5.5-6.0

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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: 2.29745444787→44.3625637794 Å / Num. obs: 24345 / % possible obs: 99.81 % / Redundancy: 21 % / Biso Wilson estimate: 55.0685253935 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1132 / Rpim(I) all: 0.02533 / Rrim(I) all: 0.1161 / Net I/σ(I): 20.55
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 20.4 % / Rmerge(I) obs: 1.946 / Mean I/σ(I) obs: 1.45 / Num. unique obs: 2406 / CC1/2: 0.577 / Rpim(I) all: 0.4367 / Rrim(I) all: 1.9996 / % possible all: 98.12

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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: Crystal structure of TkTrm10 construct ( to be deposited)

Resolution: 2.29745444787→44.3625637794 Å / SU ML: 0.312147629251 / Cross valid method: THROUGHOUT / σ(F): 1.38327623631 / Phase error: 26.7597516415
RfactorNum. reflection% reflectionSelection details
Rfree0.222729264961 1216 4.99753411146 %Random
Rwork0.195472590493 ---
obs0.196891010953 24332 99.7581074987 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 68.9272527311 Å2
Refinement stepCycle: LAST / Resolution: 2.29745444787→44.3625637794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3986 0 93 78 4157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002000548214724165
X-RAY DIFFRACTIONf_angle_d0.524789909955635
X-RAY DIFFRACTIONf_chiral_restr0.0457912640862632
X-RAY DIFFRACTIONf_plane_restr0.00257300626663705
X-RAY DIFFRACTIONf_dihedral_angle_d12.62415566082470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2975-2.38940.3177488294231320.301466738952514X-RAY DIFFRACTION98.2912332838
2.3894-2.49820.3332037092311340.2816049475522558X-RAY DIFFRACTION99.8146088246
2.4982-2.62990.3439507650141370.2810470005862593X-RAY DIFFRACTION99.8536942209
2.6299-2.79460.294079515631340.2519163267782552X-RAY DIFFRACTION99.9627837737
2.7946-3.01030.2522764991191350.2407011228052567X-RAY DIFFRACTION100
3.0103-3.31320.2501869696011360.2200429978542581X-RAY DIFFRACTION100
3.3132-3.79240.209332969011360.1854277106732574X-RAY DIFFRACTION100
3.7924-4.77710.1901069122811360.1567761041932584X-RAY DIFFRACTION100
4.7771-44.37080.1871312021741360.1699186544292593X-RAY DIFFRACTION99.8901903367
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)
16.6839588056-1.54503359549-2.762608546344.684591994630.8440994134886.210620853260.09627369068780.1203541854960.4585018211210.02915518586960.201090331828-0.2175065737610.459783133145-0.363325625065-0.1933846481760.363498452026-0.0696794500927-0.102971193650.478266772830.0300580739630.479547964793-6.94703862293-26.1705345242-12.2671244347
27.167406803480.243696860931.627059681363.559630797880.7251393904396.66789101375-0.0183125065742-0.477629419079-0.2139424196710.255475178217-0.04832933160880.228647895518-0.112027719171-0.831885142120.03332932467830.4595547841670.0148239954547-0.07340753117610.5638935011060.1338298382220.423681977455-13.0156776599-21.1889075657-8.45191264458
36.57504582007-0.8003367401683.870005508822.07677303807-0.9227069233776.891096996270.1425509543042.236973012851.07153046471-0.376047084488-0.404755003132-1.41837875829-0.7809640097262.55946393240.1895908800790.716259623489-0.09755574801610.07980838348971.372107368080.2517726992990.8225067291963.70266213795-17.6267939034-13.1601247804
48.47064214521-1.742071523195.135537967955.49662312803-1.137018813227.33044645148-0.248968273433-0.1226421996550.2758566834540.1018874183330.00563963211495-0.11049913266-0.734318887771-0.02301763348160.197388463710.423682118393-0.0306591600592-0.08128115420080.439833218529-0.03457385373510.332676597752-3.62915478273-18.33501983090.0934704576087
54.81699687521-4.92352653478-5.556784395646.744858567734.107211550378.10185756047-0.197278567722-0.04103298895790.3650207083180.6776680406280.346664207167-0.599318341231.15267632352-0.0770161565071-0.02312969840410.558091121183-0.0120405316437-0.1001922769650.3857187416680.02546582302170.43587194479117.5210799147-39.3392004858-1.01210602439
67.04269687229-2.512701765790.9749519581059.231303603351.163472105299.76213985658-0.0457761015939-0.339596000677-1.129026132960.5837310154640.1099896012010.7642379622461.91050913273-0.2759016264490.02269655327670.804386183895-0.0525307913258-0.01488338171720.4280217965240.08553099571240.66718117470617.362907674-46.87576158490.594484969246
74.38873071109-2.400627689062.549082992734.25476505949-3.178848980549.36506593051-0.1421559827750.1517078097840.2337866262510.1032142750750.00107578792618-0.376637029172-0.07346253279190.8052015758260.1513236116270.388720708523-0.0216622748345-0.01189746910760.446236477185-0.01365789618120.39206070523825.4550883533-36.1059836962-11.2502662058
86.001636129550.184874014716-1.023296950899.45206536526-0.7917340016846.913515335730.3875496166110.4720432814571.056840740370.1751651309640.2741757374310.875478736025-0.216119605099-1.18316316649-0.4987004733060.447459015172-0.1048146343430.09818471671840.6542217501990.2429336699120.597915542329.25180895748-15.5503178526-34.3323633541
96.72270050623-0.8957975126311.704116852282.55516258859-2.265161592252.259326418530.2962671488590.2734627136720.2404440029360.3552709910810.5795468969481.034999219050.665790666669-1.19105045814-0.7091675175640.593503588014-0.1368715672070.05237625134640.846606606940.2095197991190.687515537425.0218255177-20.0130520458-33.231997851
105.62451766671-5.108622353914.78543492844.66068050383-4.372713623844.08675675504-0.7342578942780.381926420266-0.08678392819930.6928413578771.166190361951.69289911158-0.886558813755-1.19441206462-0.4409059412970.702835066566-0.005374701400370.03531714922841.029038332640.3799016232640.9083925497031.83924152736-21.5066253241-32.1412616142
119.532381572074.32833237197-4.793425890284.02049174364-4.246674691914.46657168996-0.4426771413980.4868427109950.0443200006486-0.7569351304970.111859976644-0.3344735332080.8503681113920.3452069445240.3093887798760.594432725014-0.05098112804870.04385888250050.6209499988160.04772917321520.45746482481518.2946446027-27.0994261054-40.2755041984
126.21575133741-1.73362060314-3.646391169017.97674224126-4.718250533176.96753553495-0.2723811249460.3601890174830.230346271755-0.2437200768530.208023183633-0.7079411291740.2103794186420.0725404119798-0.08589741064240.449135697945-0.1550998554490.04326322483610.5709949368380.1307018553940.39936517703818.8102231683-20.2581860195-39.4806189677
134.099114295660.546086359621-2.915267593775.97463910449-3.826892696436.19657717737-0.1399190667690.6696092725250.546810747439-0.2741647872470.3014611697130.1116376449910.250804724166-0.295899741471-0.2116577871250.419706877807-0.107265112334-0.01721942174840.7447814269880.1798025294910.50519815689217.4961393356-16.5268142414-46.9510005352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 98 through 131 )
2X-RAY DIFFRACTION2chain 'A' and (resid 132 through 202 )
3X-RAY DIFFRACTION3chain 'A' and (resid 203 through 214 )
4X-RAY DIFFRACTION4chain 'A' and (resid 215 through 272 )
5X-RAY DIFFRACTION5chain 'B' and (resid 98 through 132 )
6X-RAY DIFFRACTION6chain 'B' and (resid 133 through 158 )
7X-RAY DIFFRACTION7chain 'B' and (resid 159 through 272 )
8X-RAY DIFFRACTION8chain 'C' and (resid 99 through 132 )
9X-RAY DIFFRACTION9chain 'C' and (resid 133 through 151 )
10X-RAY DIFFRACTION10chain 'C' and (resid 152 through 165 )
11X-RAY DIFFRACTION11chain 'C' and (resid 166 through 190 )
12X-RAY DIFFRACTION12chain 'C' and (resid 191 through 218 )
13X-RAY DIFFRACTION13chain 'C' and (resid 219 through 272 )

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