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- PDB-7mjz: The structure of MiaB with pentasulfide bridge -

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Basic information

Entry
Database: PDB / ID: 7mjz
TitleThe structure of MiaB with pentasulfide bridge
ComponentstRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
KeywordsTRANSFERASE / tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
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
Methylthiotransferase, N-terminal 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 ...Methylthiotransferase, N-terminal 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 / Radical SAM, alpha/beta horseshoe / TRAM domain / TRAM domain profile. / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PENTASULFIDE-SULFUR / IRON/SULFUR CLUSTER / tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1875
Polymers51,3001
Non-polymers8874
Water7,080393
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-69 kcal/mol
Surface area18650 Å2
Unit cell
Length a, b, c (Å)54.215, 81.125, 118.326
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 51300.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria)
Gene: miaB_1, miaB, B5G17_18130, BHV79_15055, Bun01g_07690, DW729_16250, DW758_11640, DW988_00575, DWW83_14680, DXB64_10975, DXC91_18100, ERS852462_00484, ERS852554_01670, GAQ56_01605, GAQ70_01795, ...Gene: miaB_1, miaB, B5G17_18130, BHV79_15055, Bun01g_07690, DW729_16250, DW758_11640, DW988_00575, DWW83_14680, DXB64_10975, DXC91_18100, ERS852462_00484, ERS852554_01670, GAQ56_01605, GAQ70_01795, GAQ72_10630, GAQ75_03160
Production host: Escherichia coli (E. coli)
References: UniProt: A0A174GYG1, tRNA-2-methylthio-N6-dimethylallyladenosine synthase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PS5 / PENTASULFIDE-SULFUR


Mass: 160.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: S5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M potassium formate, pH 7.3, 20% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.078 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 7, 2015
RadiationMonochromator: 1.078 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 38918 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 27.72 Å2 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.056 / Rrim(I) all: 0.151 / Χ2: 1.093 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.02-2.066.70.85818800.8040.3540.9290.92999.9
2.06-2.16.70.81819370.8240.3360.8861.08699.8
2.1-2.156.80.66619070.9010.2720.721100
2.15-2.26.90.56819180.9220.2320.6141.025100
2.2-2.256.90.52719360.9290.2150.571.13699.9
2.25-2.3170.49219040.9360.1990.5311.17299.8
2.31-2.3870.40919340.9480.1650.4421.12699.9
2.38-2.467.10.34419330.970.1380.3721.085100
2.46-2.547.10.31619080.970.1270.3411.10299.9
2.54-2.657.10.24919480.9750.10.2681.128100
2.65-2.777.10.2119380.9820.0840.2261.15699.9
2.77-2.917.20.16319260.990.0650.1751.144100
2.91-3.17.30.12619610.9940.050.1361.249100
3.1-3.337.30.09619630.9950.0380.1031.329100
3.33-3.677.30.06719610.9980.0260.0721.293100
3.67-4.27.30.05319890.9980.0210.0571.082100
4.2-5.297.20.04220130.9990.0170.0450.949100
5.29-506.80.04121310.9990.0170.0451.02599.9

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Processing

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

2qgq


Resolution: 2.08→29.68 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 1999 6.21 %
Rwork0.1821 30175 -
obs0.1846 32174 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.63 Å2 / Biso mean: 38.3089 Å2 / Biso min: 15.74 Å2
Refinement stepCycle: final / Resolution: 2.08→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 22 393 3905
Biso mean--40.58 41.72 -
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023602
X-RAY DIFFRACTIONf_angle_d0.5674879
X-RAY DIFFRACTIONf_dihedral_angle_d20.7961360
X-RAY DIFFRACTIONf_chiral_restr0.043553
X-RAY DIFFRACTIONf_plane_restr0.005634
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 (%)
2.08-2.130.28471370.24792064220198
2.13-2.190.2611400.229821192259100
2.19-2.250.26781420.222821342276100
2.25-2.320.23221410.214421292270100
2.32-2.410.27251390.206221082247100
2.41-2.50.30071430.206721492292100
2.5-2.620.23951410.196121312272100
2.62-2.750.24391410.1921472288100
2.75-2.930.23551430.190721372280100
2.93-3.150.25531440.197321862330100
3.15-3.470.24561430.186821672310100
3.47-3.970.22591440.169821632307100
3.97-50.15161470.144522212368100
5-29.680.17221540.157823202474100
Refinement TLS params.Method: refined / Origin x: 1.6345 Å / Origin y: 31.6155 Å / Origin z: 13.2902 Å
111213212223313233
T0.1865 Å2-0.0083 Å20.0237 Å2-0.1928 Å2-0.0281 Å2--0.1815 Å2
L2.3772 °2-0.2679 °20.6434 °2-1.3701 °2-0.2993 °2--1.0739 °2
S-0.0458 Å °0.2206 Å °0.1863 Å °-0.1806 Å °0.0379 Å °-0.0369 Å °-0.0126 Å °0.0747 Å °0.0094 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA14 - 457
2X-RAY DIFFRACTION1allB1 - 101
3X-RAY DIFFRACTION1allS2 - 415
4X-RAY DIFFRACTION1allD1

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