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- PDB-7mjw: Methylated MiaB in the complex with 5'-deoxyadenosine, methionine... -

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Basic information

Entry
Database: PDB / ID: 7mjw
TitleMethylated MiaB in the complex with 5'-deoxyadenosine, methionine and RNA
Components
  • RNA (5'-R(*GP*GP*AP*CP*UP*GP*AP*AP*(MIA)P*AP*UP*CP*C)-3')
  • tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
KeywordsTRANSFERASE/RNA / tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase / TRANSFERASE / TRANSFERASE-RNA complex
Function / homology
Function and homology information


tRNA-2-methylthio-N6-dimethylallyladenosine synthase / methylthiotransferase activity / tRNA modification / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function
tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase MiaB / Methylthiotransferase / Methylthiotransferase, N-terminal / Methylthiotransferase, N-terminal domain superfamily / Uncharacterized protein family UPF0004 / Methylthiotransferase N-terminal domain profile. / Methylthiotransferase, conserved site / Methylthiotransferase radical SAM domain signature. / TRAM domain / TRAM domain ...tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase MiaB / Methylthiotransferase / Methylthiotransferase, N-terminal / Methylthiotransferase, N-terminal domain superfamily / Uncharacterized protein family UPF0004 / Methylthiotransferase N-terminal domain profile. / Methylthiotransferase, conserved site / Methylthiotransferase radical SAM domain signature. / TRAM domain / TRAM domain / Radical SAM, alpha/beta horseshoe / TRAM domain profile. / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM
Similarity search - Domain/homology
5'-DEOXYADENOSINE / METHIONINE / IRON/SULFUR CLUSTER / FE3-S4 methylated cluster / RNA / RNA (> 10) / tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsEsakova, O.A. / Grove, T.L. / Yennawar, N.H. / Arcinas, A.J. / Wang, B. / Krebs, C. / Almo, S.C. / Booker, S.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH (GM-122595 to S.J.B) United States
National Science Foundation (NSF, United States)NSF (MCB-1716686 to S.J.B.) United States
Howard Hughes Medical Institute (HHMI)Squire J. Booker United States
CitationJournal: Nature / Year: 2021
Title: Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB.
Authors: Esakova, O.A. / Grove, T.L. / Yennawar, N.H. / Arcinas, A.J. / Wang, B. / Krebs, C. / Almo, S.C. / Booker, S.J.
History
DepositionApr 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 6, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
M: RNA (5'-R(*GP*GP*AP*CP*UP*GP*AP*AP*(MIA)P*AP*UP*CP*C)-3')
B: tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
G: RNA (5'-R(*GP*GP*AP*CP*UP*GP*AP*AP*(MIA)P*AP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,21515
Polymers111,0164
Non-polymers2,19911
Water21,7441207
1
A: tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
M: RNA (5'-R(*GP*GP*AP*CP*UP*GP*AP*AP*(MIA)P*AP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5957
Polymers55,5082
Non-polymers1,0875
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-36 kcal/mol
Surface area19370 Å2
MethodPISA
2
B: tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
G: RNA (5'-R(*GP*GP*AP*CP*UP*GP*AP*AP*(MIA)P*AP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6208
Polymers55,5082
Non-polymers1,1126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-45 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.900, 97.413, 80.738
Angle α, β, γ (deg.)90.000, 108.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / RNA chain , 2 types, 4 molecules ABMG

#1: Protein tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase / (Dimethylallyl)adenosine tRNA methylthiotransferase MiaB / tRNA-i(6)A37 methylthiotransferase


Mass: 51275.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria)
Gene: miaB_2, miaB, DW795_02470, DW831_10175, DWW14_18715, DWX44_14905, DXC07_08890, DXC80_15965, DXD90_15595, ERS417307_03809, GAP41_19630, GAP48_15545, GAP55_16410, GAQ44_15640
Production host: Escherichia coli (E. coli)
References: UniProt: A0A174NUT3, tRNA-2-methylthio-N6-dimethylallyladenosine synthase
#2: RNA chain RNA (5'-R(*GP*GP*AP*CP*UP*GP*AP*AP*(MIA)P*AP*UP*CP*C)-3')


Mass: 4232.682 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacteroides uniformis (bacteria)

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Non-polymers , 6 types, 1218 molecules

#3: Chemical ChemComp-ZKP / FE3-S4 methylated cluster


Mass: 310.830 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH3Fe3S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1207 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium cacodylate pH 5.5, 13% PEG 4000, 1,2-butanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0033 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 308607 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 12.98 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.03 / Rrim(I) all: 0.071 / Χ2: 0.888 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.435.30.882110740.7160.4170.9770.70999.9
1.43-1.455.40.734111040.770.3450.8130.77499.9
1.45-1.495.40.569110710.8490.2670.630.8100
1.49-1.525.40.453111240.8910.2120.5010.787100
1.52-1.565.50.368110530.9150.1720.4060.869100
1.56-1.65.50.282111420.9540.1310.3110.791100
1.6-1.655.50.232111280.9680.1080.2560.837100
1.65-1.75.60.188110330.9770.0870.2080.831100
1.7-1.765.60.153111490.9820.0710.1690.869100
1.76-1.835.60.117111130.9890.0540.1290.844100
1.83-1.925.60.102111010.9870.0470.1130.944100
1.92-2.025.60.084111180.9920.0380.0921.078100
2.02-2.145.70.075111250.9910.0340.0821.283100
2.14-2.315.70.065111730.9940.030.0721.318100
2.31-2.545.70.05111170.9960.0230.0551.041100
2.54-2.915.70.042111730.9970.0190.0460.936100
2.91-3.665.70.035111980.9980.0160.0390.869100
3.66-505.50.03112900.9980.0140.0340.63299.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QGQ

2qgq


Resolution: 1.4→39.08 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1737 3070 0.99 %
Rwork0.1494 305537 -
obs0.1497 308607 78.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.51 Å2 / Biso mean: 19.6576 Å2 / Biso min: 7.55 Å2
Refinement stepCycle: final / Resolution: 1.4→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6932 562 89 1207 8790
Biso mean--11.28 29.74 -
Num. residues----908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0188026
X-RAY DIFFRACTIONf_angle_d1.84811025
X-RAY DIFFRACTIONf_dihedral_angle_d20.4253179
X-RAY DIFFRACTIONf_chiral_restr0.1651264
X-RAY DIFFRACTIONf_plane_restr0.0151329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.238590.26355876593533
1.42-1.450.2959740.24717411748542
1.45-1.470.2347860.22498573865948
1.47-1.50.2283900.21448956904650
1.5-1.530.2298890.19838988907751
1.53-1.560.2024950.18469290938553
1.56-1.590.20651020.1684100461014857
1.59-1.630.18511090.1581110821119163
1.63-1.670.19021320.1511125571268971
1.67-1.710.16011420.1464138871402979
1.71-1.760.18741560.1428154271558387
1.76-1.820.16511640.1502166861685095
1.82-1.890.19941760.1517176261780299
1.89-1.960.19521790.15441766717846100
1.96-2.050.22251750.14921769517870100
2.05-2.160.1631780.14751770717885100
2.16-2.290.1661770.14811769817875100
2.29-2.470.17041790.15091766017839100
2.47-2.720.15171770.15461767617853100
2.72-3.110.1771760.15461772117897100
3.11-3.920.18371750.13911766317838100
3.92-39.080.13751800.13061764517825100
Refinement TLS params.Method: refined / Origin x: 6.8375 Å / Origin y: 20.714 Å / Origin z: 49.8641 Å
111213212223313233
T0.0861 Å20.0075 Å20.0164 Å2-0.0796 Å20.0166 Å2--0.1208 Å2
L0.0789 °20.0289 °20.1373 °2-0.2349 °20.3519 °2--1.1413 °2
S-0.0058 Å °0.0312 Å °0.0345 Å °-0.0333 Å °0.0003 Å °0.003 Å °-0.0876 Å °-0.0021 Å °0.0057 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA17 - 501
2X-RAY DIFFRACTION1allA601
3X-RAY DIFFRACTION1allA701 - 801
4X-RAY DIFFRACTION1allM29 - 41
5X-RAY DIFFRACTION1allB17 - 501
6X-RAY DIFFRACTION1allB601
7X-RAY DIFFRACTION1allB701 - 801
8X-RAY DIFFRACTION1allG29 - 41
9X-RAY DIFFRACTION1allS3 - 1251
10X-RAY DIFFRACTION1allH1 - 4

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