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- PDB-7mjy: MiaB in the complex with s-adenosyl-L-homocysteine and RNA -

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Basic information

Entry
Database: PDB / ID: 7mjy
TitleMiaB in the complex with s-adenosyl-L-homocysteine and RNA
Components
  • RNA (5'-R(P*UP*AP*UP*UP*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


methylthiotransferase activity / tRNA-2-methylthio-N6-dimethylallyladenosine synthase / tRNA modification / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function
tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase MiaB / Methylthiotransferase, N-terminal / Methylthiotransferase N-terminal domain profile. / Uncharacterized protein family UPF0004 / Methylthiotransferase, N-terminal domain superfamily / Methylthiotransferase / Methylthiotransferase, conserved site / Methylthiotransferase radical SAM domain signature. / TRAM domain / TRAM domain ...tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase MiaB / Methylthiotransferase, N-terminal / Methylthiotransferase N-terminal domain profile. / Uncharacterized protein family UPF0004 / Methylthiotransferase, N-terminal domain superfamily / Methylthiotransferase / Methylthiotransferase, conserved site / Methylthiotransferase radical SAM domain signature. / TRAM domain / TRAM domain / TRAM domain profile. / Radical SAM, alpha/beta horseshoe / Elongator protein 3, MiaB family, Radical SAM / Elp3/MiaB/NifB / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM
Similarity search - Domain/homology
FE3-S4 CLUSTER / RNA (> 10) / RNA / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / S-ADENOSYL-L-HOMOCYSTEINE / TRIETHYLENE GLYCOL / tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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

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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(P*UP*AP*UP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,67716
Polymers55,4172
Non-polymers2,26114
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.834, 79.982, 110.137
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 / RNA chain , 2 types, 2 molecules AM

#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.: 1
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(P*UP*AP*UP*UP*C)-3')


Mass: 4141.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacteroides uniformis (bacteria)

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Non-polymers , 7 types, 200 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium cacodylate, pH 5.5, 13% PEG 4000, and 3% 1,6-hexanediol

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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: Jul 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0033 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 40640 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 19.33 Å2 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.058 / Rrim(I) all: 0.163 / Χ2: 1.048 / Net I/σ(I): 4.8 / Num. measured all: 303282
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.86-1.895.10.91819710.6810.4211.0141.09899.6
1.89-1.935.90.87420090.6950.3790.9551.08999.9
1.93-1.966.50.77519790.7890.320.8411.08699.9
1.96-26.90.62820350.870.2520.6781.081100
2-2.057.20.60519780.8770.2370.6511.087100
2.05-2.097.20.55720090.8920.220.61.084100
2.09-2.157.40.46420140.9240.180.4991.083100
2.15-2.217.70.42119770.9390.160.4521.064100
2.21-2.277.80.3620320.9530.1350.3851.075100
2.27-2.348.20.32320380.9650.1190.3451.092100
2.34-2.438.10.28119910.9740.1040.31.043100
2.43-2.528.10.24620290.9780.0910.2631.035100
2.52-2.647.90.20920160.9840.0780.2241.05100
2.64-2.787.70.17520210.9860.0660.1881.027100
2.78-2.957.80.14220430.9890.0530.1520.989100
2.95-3.188.30.11520500.9940.0420.1221.028100
3.18-3.58.10.08920510.9960.0330.0951.005100
3.5-4.017.60.07420700.9960.0280.081.014100
4.01-5.057.90.0621030.9970.0220.0640.955100
5.05-507.50.06422240.9970.0240.0691.028100

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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
Resolution: 1.86→48.37 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 2000 4.93 %
Rwork0.1741 38568 -
obs0.1758 40568 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.85 Å2 / Biso mean: 27.1878 Å2 / Biso min: 7.46 Å2
Refinement stepCycle: final / Resolution: 1.86→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3515 68 121 186 3890
Biso mean--37.13 32.21 -
Num. residues----453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063903
X-RAY DIFFRACTIONf_angle_d1.2925272
X-RAY DIFFRACTIONf_dihedral_angle_d27.1761568
X-RAY DIFFRACTIONf_chiral_restr0.059595
X-RAY DIFFRACTIONf_plane_restr0.009665
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.86-1.910.33881340.28342599273396
1.91-1.960.29851410.236927062847100
1.96-2.020.25841420.188827412883100
2.02-2.080.21511410.182927212862100
2.08-2.160.2031420.173627452887100
2.16-2.240.20871420.161527312873100
2.24-2.340.20561430.155927482891100
2.34-2.470.20571400.158327242864100
2.47-2.620.20571430.161327432886100
2.62-2.820.19281440.160227662910100
2.82-3.110.19931440.170527832927100
3.11-3.560.18621440.166527842928100
3.56-4.480.17621460.155228252971100
4.48-48.370.22271540.190929523106100

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