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- PDB-8joz: Crystal structure of CmoM from E. coli complexed with sinefungin ... -

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Basic information

Entry
Database: PDB / ID: 8joz
TitleCrystal structure of CmoM from E. coli complexed with sinefungin and cellularly expressed tRNA Ser
Components
  • tRNA 5-carboxymethoxyuridine methyltransferase
  • tRNA Ser (88-MER)
KeywordsTRANSFERASE/RNA / Methyltransferase / tRNA post-transcriptional modification / CmoM mcmo5U / TRANSFERASE-RNA complex / TRANSFERASE
Function / homology
Function and homology information


tRNA (5-carboxymethoxyuridine(34)-5-O)-methyltransferase activity / tRNA wobble uridine modification / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity
Similarity search - Function
tRNA 5-carboxymethoxyuridine methyltransferase / Methyltransferase domain / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
SINEFUNGIN / RNA / RNA (> 10) / tRNA 5-carboxymethoxyuridine methyltransferase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsYoo, J. / Kim, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structural basis for the selective methylation of 5-carboxymethoxyuridine in tRNA modification.
Authors: Yoo, J. / Lee, J. / Kim, J.
History
DepositionJun 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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 5-carboxymethoxyuridine methyltransferase
B: tRNA Ser (88-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,40010
Polymers60,8482
Non-polymers5528
Water6,323351
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.614, 65.614, 584.532
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-469-

HOH

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Components

#1: Protein tRNA 5-carboxymethoxyuridine methyltransferase / cmo5U methyltransferase


Mass: 32199.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: cmoM, smtA, ycbD, b0921, JW0904 / Plasmid: pCA24N / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P36566, Transferases; Transferring one-carbon groups; Methyltransferases
#2: RNA chain tRNA Ser (88-MER)


Mass: 28648.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Plasmid: pBSTNAV / Production host: Escherichia coli K-12 (bacteria)
#3: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.98 Å3/Da / Density % sol: 58.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.04 M Magnesium acetate tetrahydrate, 0.05 M Sodium cacodylate trihydrate pH 6.0, 30% v/v (+/-)-2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.22→40.74 Å / Num. obs: 38928 / % possible obs: 99.94 % / Redundancy: 35.6 % / CC1/2: 0.999 / Net I/σ(I): 16.92
Reflection shellResolution: 2.22→2.3 Å / Num. unique obs: 3750 / CC1/2: 0.658

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
MxDCdata collection
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Coot0.9.2model building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→40.74 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 2000 5.14 %
Rwork0.1985 --
obs0.1999 38921 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→40.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 1898 34 351 4341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064253
X-RAY DIFFRACTIONf_angle_d0.9556188
X-RAY DIFFRACTIONf_dihedral_angle_d11.8621425
X-RAY DIFFRACTIONf_chiral_restr0.045703
X-RAY DIFFRACTIONf_plane_restr0.01468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.280.30231390.27972582X-RAY DIFFRACTION100
2.28-2.340.31481380.25522537X-RAY DIFFRACTION100
2.34-2.410.31191380.24912550X-RAY DIFFRACTION100
2.41-2.480.2921380.2582560X-RAY DIFFRACTION100
2.48-2.570.30451400.24982571X-RAY DIFFRACTION100
2.57-2.680.30851390.25752564X-RAY DIFFRACTION100
2.68-2.80.30031410.24412599X-RAY DIFFRACTION100
2.8-2.940.22961410.22232605X-RAY DIFFRACTION100
2.94-3.130.24271420.20962624X-RAY DIFFRACTION100
3.13-3.370.25731420.20922618X-RAY DIFFRACTION100
3.37-3.710.19361430.18872656X-RAY DIFFRACTION100
3.71-4.250.20491460.16862694X-RAY DIFFRACTION100
4.25-5.350.18221490.15522749X-RAY DIFFRACTION100
5.35-40.740.17711640.17843012X-RAY DIFFRACTION100

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