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- PDB-6zxw: Structure of Archaeoglobus fulgidus Trm11-Trm112 m2G10 tRNA methy... -

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Basic information

Entry
Database: PDB / ID: 6zxw
TitleStructure of Archaeoglobus fulgidus Trm11-Trm112 m2G10 tRNA methyltransferase complex bound to sinefungin
Components
  • Uncharacterized protein
  • tRNA (Guanine(10)-N2)-dimethyltransferase
KeywordsRNA BINDING PROTEIN / tRNA modifications / Epitranscriptomics / Methyltransferase / Heterodimeric enzyme
Function / homology
Function and homology information


tRNA (guanine10-N2)-dimethyltransferase / tRNA (guanine(10)-N2)-dimethyltransferase activity / tRNA (guanine(10)-N2)-methyltransferase activity / : / tRNA methylation / tRNA binding / RNA binding / cytoplasm
Similarity search - Function
tRNA guanine(10)-N2-dimethyltransferase / Uncharacterized protein family UPF0020 signature. / Ribosomal RNA large subunit methyltransferase K/L-like, FLD domain / Putative RNA methylase family UPF0020 / THUMP domain / THUMP domain / THUMP domain profile. / Trm112-like / Trm112p-like protein / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
ACETIC ACID / SINEFUNGIN / Uncharacterized protein / tRNA (Guanine(10)-N2)-dimethyltransferase / tRNA (guanine(10)-N2)-dimethyltransferase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsGraille, M. / Wang, C.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Functional and structural characterization of the Trm11-Trm112 m2G10 tRNA methyltransferase complex
Authors: Wang, C. / Tran, N.V. / Jactel, V. / Guerineau, V. / Graille, M.
History
DepositionJul 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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

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Assembly

Deposited unit
G: tRNA (Guanine(10)-N2)-dimethyltransferase
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,76518
Polymers44,3852
Non-polymers1,38016
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-1 kcal/mol
Surface area17550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.360, 92.940, 101.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules GH

#1: Protein tRNA (Guanine(10)-N2)-dimethyltransferase


Mass: 37551.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: XD40_1676, XD48_1558
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A117KU88, UniProt: O29011*PLUS
#2: Protein Uncharacterized protein


Mass: 6833.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: XD40_0284, XD48_0149
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A117KMN5

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Non-polymers , 6 types, 80 molecules

#3: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 4 Å3/Da / Density % sol: 69.25 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Sodium citrate pH 6; 9% PEG 4000, 0.1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.19→39.55 Å / Num. obs: 36999 / % possible obs: 99.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 66.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.1
Reflection shellResolution: 2.19→2.33 Å / Rmerge(I) obs: 1.231 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5852 / CC1/2: 0.522 / % possible all: 98.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZXV
Resolution: 2.19→39.55 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.155 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.139
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1850 5 %RANDOM
Rwork0.198 ---
obs0.199 36995 99.7 %-
Displacement parametersBiso max: 172.57 Å2 / Biso mean: 72.26 Å2 / Biso min: 41.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.6664 Å20 Å20 Å2
2---4.2406 Å20 Å2
3---3.5742 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 2.19→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3037 0 86 64 3187
Biso mean--78.14 64.68 -
Num. residues----378
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1154SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes537HARMONIC5
X-RAY DIFFRACTIONt_it3162HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion396SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3451SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3162HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4240HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion20.95
LS refinement shellResolution: 2.19→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2643 37 5 %
Rwork0.2665 703 -
all0.2664 740 -
obs--95.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.67620.4141-0.73431.5736-0.77261.82910.0617-0.06510.09050.0308-0.17930.0134-0.07650.0720.1176-0.17620.0091-0.0428-0.1267-0.0068-0.15562.0351-16.4088-6.8143
24.62680.6703-0.272511.21540.55513.91760.1489-0.012-1.08850.4135-0.1845-0.80141.08850.38560.0356-0.03240.1485-0.004-0.36090.2753-0.03622.7487-48.12485.2711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ G|* }G1 - 321
2X-RAY DIFFRACTION2{ H|* }H1 - 57

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