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

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Basic information

Entry
Database: PDB / ID: 6ems
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 (adenine9-N1)-methyltransferase / tRNA (adenine(9)-N1)-methyltransferase activity / 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
tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.996 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


Theoretical massNumber of molelcules
Total (without water)42,2181
Polymers42,2181
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.687, 65.925, 67.044
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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


Mass: 42217.750 Da / Num. of mol.: 1 / Mutation: C77A, C120A
Source method: isolated from a genetically manipulated source
Details: This is a c-terminal deletion construct of the protein
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.42 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 18% PEG3350 and 0.1M Tris pH 7.5 / PH range: 7-7.5

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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: 1.996→47.0066469139 Å / Num. obs: 20375 / % possible obs: 99.97 % / Redundancy: 19.9 % / Biso Wilson estimate: 49.0376106091 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.07567 / Rpim(I) all: 0.0174 / Rrim(I) all: 0.0777 / Net I/σ(I): 24.82
Reflection shellResolution: 1.996→2.067 Å / Redundancy: 20.1 % / Rmerge(I) obs: 2.289 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1976 / CC1/2: 0.821 / Rpim(I) all: 0.5138 / Rrim(I) all: 2.348 / % possible all: 99.85

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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: 5a7y

5a7y


Resolution: 1.996→47.007 Å / SU ML: 0.26777404931 / Cross valid method: THROUGHOUT / σ(F): 1.327 / Phase error: 26.4225135098
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 1016 4.98650306748 %RANDOM
Rwork0.196 ---
obs0.198 20375 99.9509443218 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 61.6575465554 Å2
Refinement stepCycle: LAST / Resolution: 1.996→47.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 0 65 1993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00443134713671967
X-RAY DIFFRACTIONf_angle_d0.6167420364812654
X-RAY DIFFRACTIONf_chiral_restr0.0470679659226292
X-RAY DIFFRACTIONf_plane_restr0.00342955984398338
X-RAY DIFFRACTIONf_dihedral_angle_d13.82499851111177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9955-2.10070.345243324421410.3018899485282685X-RAY DIFFRACTION99.7529121073
2.1007-2.23230.288033644961410.268666359092734X-RAY DIFFRACTION100
2.2323-2.40470.3149501158551420.2509756899152730X-RAY DIFFRACTION100
2.4047-2.64670.2325393437371450.2188722608542740X-RAY DIFFRACTION100
2.6467-3.02960.2756366295511470.2179530975672768X-RAY DIFFRACTION100
3.0296-3.81670.2054041491781460.1946672496212777X-RAY DIFFRACTION99.9658002736
3.8167-47.01970.2282881395041540.1691151462582925X-RAY DIFFRACTION99.935086011
Refinement TLS params.Method: refined / Origin x: 25.6911600187 Å / Origin y: 37.1920787861 Å / Origin z: 34.5003053449 Å
111213212223313233
T0.307124651728 Å20.0284423520709 Å2-0.00930741649947 Å2-0.337036524806 Å20.0453034782397 Å2--0.227958219216 Å2
L2.83086169799 °21.97497882402 °2-0.108855116026 °2-4.7218970489 °20.650264402339 °2--2.01892550817 °2
S0.190579602228 Å °-0.0254877524324 Å °0.135586433125 Å °0.0462336485289 Å °-0.102447011537 Å °-0.0063889470877 Å °-0.169680016586 Å °0.0828962167769 Å °-0.0838536891081 Å °
Refinement TLS groupSelection details: all

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