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- PDB-7mjx: MiaB in the complex with 5'-deoxyadenosine, methionine and RNA -

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Basic information

Entry
Database: PDB / ID: 7mjx
TitleMiaB 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-N(6)-dimethylallyladenosine(37) synthase activity / tRNA-2-methylthio-N6-dimethylallyladenosine synthase / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
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 / Radical SAM, alpha/beta horseshoe ...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
Similarity search - Domain/homology
5'-DEOXYADENOSINE / FE3-S4 CLUSTER / METHIONINE / 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: 1.5 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
B: tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
D: RNA (5'-R(*GP*GP*AP*CP*UP*GP*AP*AP*(MIA)P*AP*UP*CP*C)-3')
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)113,30316
Polymers111,0164
Non-polymers2,28712
Water25,8151433
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)56,6028
Polymers55,5082
Non-polymers1,0946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-70 kcal/mol
Surface area18570 Å2
MethodPISA
2
B: tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
D: 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)56,7018
Polymers55,5082
Non-polymers1,1936
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-56 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.690, 97.120, 80.606
Angle α, β, γ (deg.)90.000, 108.100, 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 ABDM

#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 , 7 types, 1445 molecules

#3: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1433 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium 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 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: 1.5→50 Å / Num. obs: 143421 / % possible obs: 89.3 % / Redundancy: 2 % / Biso Wilson estimate: 11.77 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.044 / Rrim(I) all: 0.071 / Χ2: 0.931 / Net I/σ(I): 10.1 / Num. measured all: 289708
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.531.70.24488860.8720.2120.3250.74783.4
1.53-1.571.90.21295440.9050.1760.2770.74289.1
1.57-1.622.10.19497890.9240.1540.2490.81592
1.62-1.662.10.16898270.9420.1350.2170.85292
1.66-1.722.10.14497620.9530.1160.1860.87891.2
1.72-1.7820.12395280.9660.10.1590.94389.5
1.78-1.851.90.10193940.9740.0860.1330.99388.1
1.85-1.931.90.08994430.9790.0750.1161.03188.5
1.93-2.0420.07493660.9830.0620.0971.17287.3
2.04-2.1620.06794290.9860.0550.0871.05588.1
2.16-2.3320.05994240.9890.0490.0770.97788.2
2.33-2.561.90.05493450.990.0450.070.96487.2
2.56-2.9420.04895040.9920.040.0630.99288.4
2.94-3.72.20.04299220.9940.0330.0540.91392.2
3.7-502.30.04102580.9940.0310.0510.90394.1

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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: 1.5→41.02 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 16.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1701 2000 1.39 %
Rwork0.1485 141390 -
obs0.1488 143390 89.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.98 Å2 / Biso mean: 17.4132 Å2 / Biso min: 6.36 Å2
Refinement stepCycle: final / Resolution: 1.5→41.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6941 562 95 1433 9031
Biso mean--11.11 28.28 -
Num. residues----909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0188097
X-RAY DIFFRACTIONf_angle_d2.04211131
X-RAY DIFFRACTIONf_dihedral_angle_d21.8543212
X-RAY DIFFRACTIONf_chiral_restr0.1671272
X-RAY DIFFRACTIONf_plane_restr0.0161349
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 (%)
1.5-1.540.25941330.21119346947983
1.54-1.580.23121430.1837101191026290
1.58-1.620.20981450.1686103491049492
1.62-1.680.1941490.1657104201056992
1.68-1.740.19471440.1591102171036191
1.74-1.810.18341410.1534100311017288
1.81-1.890.17081430.1501100151015889
1.89-1.990.19231390.15039833997287
1.99-2.110.17211400.152899631010388
2.11-2.280.15991410.144499661010788
2.28-2.510.16061400.149198681000887
2.51-2.870.15141410.1517100091015088
2.87-3.610.16891470.1397104331058092
3.61-41.020.14391540.1302108211097594
Refinement TLS params.Method: refined / Origin x: 36.717 Å / Origin y: 7.1073 Å / Origin z: 26.8808 Å
111213212223313233
T0.066 Å2-0.0099 Å20.0126 Å2-0.0675 Å2-0.0134 Å2--0.1054 Å2
L0.0689 °2-0.029 °20.1288 °2-0.206 °2-0.2998 °2--1.0216 °2
S-0.0036 Å °-0.0264 Å °0.0229 Å °0.0236 Å °0.004 Å °-0.0011 Å °-0.0628 Å °-0.0033 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA16 - 457
2X-RAY DIFFRACTION1allA501 - 601
3X-RAY DIFFRACTION1allB17 - 457
4X-RAY DIFFRACTION1allB601 - 701
5X-RAY DIFFRACTION1allG2
6X-RAY DIFFRACTION1allD29 - 41
7X-RAY DIFFRACTION1allM29 - 41
8X-RAY DIFFRACTION1allC1 - 2
9X-RAY DIFFRACTION1allE1
10X-RAY DIFFRACTION1allH2
11X-RAY DIFFRACTION1allK2 - 5
12X-RAY DIFFRACTION1allS1 - 1660

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