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- PDB-6qe6: Structure of M. capricolum TrmK in complex with the natural cofac... -

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Basic information

Entry
Database: PDB / ID: 6qe6
TitleStructure of M. capricolum TrmK in complex with the natural cofactor product S-adenosyl-homocysteine (SAH)
ComponentstRNA (Adenine(22)-N(1))-methyltransferase
KeywordsTRANSFERASE / RNA MTases / methyltransferase / m6A / transition state analogue / inhibitor / RNA binding / TrmK / RlmJ / m1A / structure.
Function / homologytRNA (adenine22-N1)-methyltransferase / tRNA methyltransferase TrmK / tRNA (adenine(22)-N(1))-methyltransferase / : / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / tRNA (Adenine(22)-N(1))-methyltransferase
Function and homology information
Biological speciesMycoplasma capricolum subsp. capricolum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsOerum, S. / Catala, M. / Atdjian, C. / Brachet, F. / Ponchon, L. / Barraud, P. / Iannazzo, L. / Droogmans, L. / Braud, E. / Etheve-Quelquejeu, M. / Tisne, C.
CitationJournal: Rna Biol. / Year: 2019
Title: Bisubstrate analogues as structural tools to investigate m6A methyltransferase active sites.
Authors: Oerum, S. / Catala, M. / Atdjian, C. / Brachet, F. / Ponchon, L. / Barraud, P. / Iannazzo, L. / Droogmans, L. / Braud, E. / Etheve-Quelquejeu, M. / Tisne, C.
History
DepositionJan 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (Adenine(22)-N(1))-methyltransferase
B: tRNA (Adenine(22)-N(1))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7904
Polymers57,0212
Non-polymers7692
Water3,369187
1
A: tRNA (Adenine(22)-N(1))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8952
Polymers28,5111
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA (Adenine(22)-N(1))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8952
Polymers28,5111
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.760, 131.090, 58.470
Angle α, β, γ (deg.)90.00, 103.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein tRNA (Adenine(22)-N(1))-methyltransferase


Mass: 28510.572 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma capricolum subsp. capricolum (bacteria)
Gene: trmK, MCGM508_03695 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0C3A3T0, tRNA (adenine22-N1)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Li2SO4, 0.1 M HEPES pH 7.5, 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jun 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.36→42.91 Å / Num. obs: 24468 / % possible obs: 99.75 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.2719 / Net I/σ(I): 5.47
Reflection shellResolution: 2.36→2.44 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BLV

4blv


Resolution: 2.36→42.909 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2514 1251 5.12 %
Rwork0.1847 --
obs0.1881 24455 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.36→42.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3724 0 52 187 3963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083850
X-RAY DIFFRACTIONf_angle_d0.9065216
X-RAY DIFFRACTIONf_dihedral_angle_d8.2312316
X-RAY DIFFRACTIONf_chiral_restr0.053596
X-RAY DIFFRACTIONf_plane_restr0.004652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3601-2.45460.3521350.2632586X-RAY DIFFRACTION99
2.4546-2.56630.31231430.25432551X-RAY DIFFRACTION100
2.5663-2.70160.35621330.24262579X-RAY DIFFRACTION100
2.7016-2.87080.32691420.22742561X-RAY DIFFRACTION100
2.8708-3.09240.2911350.22342574X-RAY DIFFRACTION100
3.0924-3.40350.28711330.18882589X-RAY DIFFRACTION100
3.4035-3.89570.23131430.16012576X-RAY DIFFRACTION100
3.8957-4.9070.17991460.14192576X-RAY DIFFRACTION100
4.907-42.91590.21781410.16082612X-RAY DIFFRACTION100

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