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- PDB-7mjv: MiaB in the complex with s-adenosylmethionine and RNA -

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Basic information

Entry
Database: PDB / ID: 7mjv
TitleMiaB in the complex with s-adenosylmethionine and RNA
Components
  • RNA (5'-R(P*AP*GP*GP*AP*CP*UP*GP*AP*AP*(ZJS)P*AP*UP*CP*CP*U)-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
FE3-S4 CLUSTER / S-ADENOSYLMETHIONINE / IRON/SULFUR 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: 2.24 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
E: RNA (5'-R(P*AP*GP*GP*AP*CP*UP*GP*AP*AP*(ZJS)P*AP*UP*CP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8737
Polymers56,7792
Non-polymers1,0945
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-74 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.155, 81.442, 109.751
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 AE

#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*AP*GP*GP*AP*CP*UP*GP*AP*AP*(ZJS)P*AP*UP*CP*CP*U)-3')


Mass: 5503.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacteroides uniformis (bacteria)

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Non-polymers , 5 types, 42 molecules

#3: 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
#4: 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
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.13 Å3/Da / Density % sol: 42.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM Na-cacodylate, pH 5.5, 13% PEG 4000 and 3% (+/-)-2-methyl-2,4-pentanediol

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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 EIGER2 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: 2.24→50 Å / Num. obs: 22398 / % possible obs: 93.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 31.73 Å2 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.058 / Rrim(I) all: 0.164 / Χ2: 1.021 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.3340.54316090.9050.250.61.05668.4
2.33-2.424.50.52218450.930.2340.5741.05279.5
2.42-2.5350.4921800.9580.2170.5371.03992.3
2.53-2.676.50.48722870.9650.1980.5271.04997.8
2.67-2.837.90.40723720.9760.1540.4361.04799.3
2.83-3.059.10.32323490.9880.1150.3441.02599.5
3.05-3.369.10.20223920.9930.0720.2151.03199.7
3.36-3.858.40.12923870.9940.0480.1380.98399.7
3.85-4.858.50.09224160.9950.0340.0990.97399.6
4.85-508.40.08725610.9960.0310.0931.01899.6

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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: 2.24→45.51 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2726 1997 8.96 %
Rwork0.243 20296 -
obs0.2456 22293 92.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.7 Å2 / Biso mean: 59.7606 Å2 / Biso min: 30.19 Å2
Refinement stepCycle: final / Resolution: 2.24→45.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 326 44 37 3894
Biso mean--42.88 48.27 -
Num. residues----459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083957
X-RAY DIFFRACTIONf_angle_d1.8875425
X-RAY DIFFRACTIONf_dihedral_angle_d23.406683
X-RAY DIFFRACTIONf_chiral_restr0.074625
X-RAY DIFFRACTIONf_plane_restr0.024643
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.24-2.30.3881850.299787357
2.3-2.360.32421140.2851115074
2.36-2.430.3161230.293125283
2.43-2.510.35961410.2804141491
2.51-2.60.35461430.2817147296
2.6-2.70.26881530.2688153799
2.7-2.820.32511500.2758152899
2.82-2.970.2961520.2759154299
2.97-3.160.28341520.2607154799
3.16-3.40.26511540.24831562100
3.4-3.740.27241520.23861553100
3.74-4.280.21661560.21661585100
4.28-5.390.26131560.20471594100
5.4-45.510.24571660.22491687100
Refinement TLS params.Method: refined / Origin x: 24.0822 Å / Origin y: 2.7182 Å / Origin z: 119.7102 Å
111213212223313233
T0.2867 Å20.0226 Å20.0187 Å2-0.4291 Å2-0.0804 Å2--0.6558 Å2
L2.8837 °20.4819 °2-0.4005 °2-2.1949 °20.6549 °2--1.3006 °2
S-0.006 Å °0.6672 Å °-0.0001 Å °-0.4201 Å °0.0395 Å °-0.1115 Å °-0.1497 Å °-0.0283 Å °-0.0268 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA14 - 457
2X-RAY DIFFRACTION1allA501
3X-RAY DIFFRACTION1allB2
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allE28 - 42
6X-RAY DIFFRACTION1allD1 - 3
7X-RAY DIFFRACTION1allS1 - 46

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