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- PDB-6zxv: Structure of Archaeoglobus fulgidus Trm11 m2G10 tRNA methyltransf... -

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Basic information

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


tRNA (guanine10-N2)-dimethyltransferase / : / 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
SINEFUNGIN / tRNA (Guanine(10)-N2)-dimethyltransferase / tRNA (guanine(10)-N2)-dimethyltransferase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.88 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA (Guanine(10)-N2)-dimethyltransferase
B: tRNA (Guanine(10)-N2)-dimethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8778
Polymers77,8662
Non-polymers1,0116
Water3,531196
1
A: tRNA (Guanine(10)-N2)-dimethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5005
Polymers38,9331
Non-polymers5684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA (Guanine(10)-N2)-dimethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3763
Polymers38,9331
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.553, 74.172, 112.894
Angle α, β, γ (deg.)90.000, 93.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 38932.879 Da / Num. of mol.: 2
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: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Hepes pH 7, 0.8 M KNaTartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980096 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980096 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 54554 / % possible obs: 98.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 33.78 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.113 / Net I/σ(I): 10.2
Reflection shellResolution: 1.88→2 Å / Rmerge(I) obs: 1.103 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8304 / CC1/2: 0.585

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 1.88→21.68 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.169 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.154
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2725 5 %RANDOM
Rwork0.223 ---
obs0.225 54497 98.3 %-
Displacement parametersBiso max: 123.32 Å2 / Biso mean: 39.11 Å2 / Biso min: 17.53 Å2
Baniso -1Baniso -2Baniso -3
1-4.5026 Å20 Å2-4.5089 Å2
2--2.2956 Å20 Å2
3----6.7981 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 1.88→21.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5219 0 70 196 5485
Biso mean--35.99 41.57 -
Num. residues----648
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2007SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes950HARMONIC5
X-RAY DIFFRACTIONt_it5456HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion687SEMIHARMONIC5
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_contact6461SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5456HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7363HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.56
X-RAY DIFFRACTIONt_other_torsion19.04
LS refinement shellResolution: 1.88→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2394 55 5.05 %
Rwork0.2529 1035 -
all0.2522 1090 -
obs--66.75 %
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)
10.9069-0.0901-0.17620.55150.55310.92060.04210.139-0.0295-0.0851-0.06410.0228-0.073-0.06910.0220.04230.01740.0465-0.00540.0178-0.256911.61720.520948.6354
20.478-0.2287-0.17660.47250.35690.81080.00680.024-0.04830.0075-0.00710.01720.0126-0.0030.00020.04370.01990.02350.0434-0.0078-0.2265-5.699722.48188.4364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-3 - 321
2X-RAY DIFFRACTION2{ B|* }B-1 - 321

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