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- PDB-7o4o: Structure of Staphylococcus aureus m1A22-tRNA methyltransferase i... -

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Basic information

Entry
Database: PDB / ID: 7o4o
TitleStructure of Staphylococcus aureus m1A22-tRNA methyltransferase in complex with S-adenosylhomocysteine
ComponentstRNA (Adenine(22)-N(1))-methyltransferase
KeywordsRNA BINDING PROTEIN / tRNA / methyltransferase / Staphylococcus aureus
Function / homologytRNA (adenine22-N1)-methyltransferase / tRNA (adenine(22)-N1)-methyltransferase activity / tRNA methyltransferase TrmK / tRNA (adenine(22)-N(1))-methyltransferase / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / tRNA (Adenine-N(1))-methyltransferase
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsGloster, T.M. / Czekster, C.M. / da Silva, R.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust208980/Z/17/Z United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structure, dynamics, and molecular inhibition of the Staphylococcus aureus m 1 A22-tRNA methyltransferase TrmK.
Authors: Sweeney, P. / Galliford, A. / Kumar, A. / Raju, D. / Krishna, N.B. / Sutherland, E. / Leo, C.J. / Fisher, G. / Lalitha, R. / Muthuraj, L. / Sigamani, G. / Oehler, V. / Synowsky, S. / ...Authors: Sweeney, P. / Galliford, A. / Kumar, A. / Raju, D. / Krishna, N.B. / Sutherland, E. / Leo, C.J. / Fisher, G. / Lalitha, R. / Muthuraj, L. / Sigamani, G. / Oehler, V. / Synowsky, S. / Shirran, S.L. / Gloster, T.M. / Czekster, C.M. / Kumar, P. / da Silva, R.G.
History
DepositionApr 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 6, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 1, 2024Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,1634
Polymers25,5941
Non-polymers5693
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-1 kcal/mol
Surface area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.750, 61.440, 63.190
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 (Adenine(22)-N(1))-methyltransferase / tRNA (Adenine-N(1))-methyltransferase / tRNA methyltransferase / tRNA-m1A22 methylase


Mass: 25594.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: trmK, BTN44_04370, DD547_01646, DQV53_08725, EP54_01080, EQ90_01915, FA040_08445, G0X12_13870, G6Y10_03490, GO746_11460, GO803_02410, GO821_00660, GO894_13820, GO942_05350, HMPREF2819_12705, ...Gene: trmK, BTN44_04370, DD547_01646, DQV53_08725, EP54_01080, EQ90_01915, FA040_08445, G0X12_13870, G6Y10_03490, GO746_11460, GO803_02410, GO821_00660, GO894_13820, GO942_05350, HMPREF2819_12705, HMPREF3211_01711, NCTC10654_01624, NCTC10988_01882, SAMEA1029528_01600, SAMEA1029547_00798, SAMEA1029553_00619, SAMEA103891215_02131, SAMEA103891286_01600, SAMEA103891321_01985, SAMEA103891529_00207, SAMEA1964876_01370, SAMEA1965205_01483, SAMEA1966505_01613, SAMEA1969349_01355, SAMEA1969845_01762, SAMEA1971706_00969, SAMEA1972827_01752, SAMEA2076212_01686, SAMEA2076218_01752, SAMEA2076220_01838, SAMEA2076226_01470, SAMEA2076463_01221, SAMEA2076464_01220, SAMEA2076470_01440, SAMEA2076472_01358, SAMEA2076478_01562, SAMEA2076480_01089, SAMEA2076481_01742, SAMEA2076743_01499, SAMEA2076745_01827, SAMEA2076746_01427, SAMEA2076747_01232, SAMEA2076749_01543, SAMEA2076751_01354, SAMEA2076752_01303, SAMEA2076755_00992, SAMEA2076756_01055, SAMEA2076758_00894, SAMEA2076759_01126, SAMEA2076761_01348, SAMEA2076762_01436, SAMEA2076763_00759, SAMEA2076764_01515, SAMEA2076765_01533, SAMEA2077023_01670, SAMEA2077025_00820, SAMEA2077027_01445, SAMEA2077029_01261, SAMEA2077031_01378, SAMEA2077034_01301, SAMEA2077035_01224, SAMEA2077039_01360, SAMEA2077040_01028, SAMEA2077041_01644, SAMEA2077044_01316, SAMEA2077045_01391, SAMEA2077046_01185, SAMEA2077293_01519, SAMEA2077294_01624, SAMEA2077295_01192, SAMEA2077297_01318, SAMEA2077300_01622, SAMEA2077301_01189, SAMEA2077302_01534, SAMEA2077303_01399, SAMEA2077307_01350, SAMEA2077832_01495, SAMEA2078252_01643, SAMEA2078256_01246, SAMEA2078307_01427, SAMEA2078308_01217, SAMEA2078553_01120, SAMEA2078558_01423, SAMEA2078560_01322, SAMEA2078569_01685, SAMEA2078570_01555, SAMEA2078572_01773, SAMEA2078824_01091, SAMEA2078837_01341, SAMEA2079048_01436, SAMEA2079051_01539, SAMEA2079277_01894, SAMEA2079291_01924, SAMEA2079503_01584, SAMEA2079507_01091, SAMEA2079512_01790, SAMEA2079517_01641, SAMEA2079724_01423, SAMEA2079727_01698, SAMEA2079728_01857, SAMEA2079732_01742, SAMEA2079946_01710, SAMEA2079949_01677, SAMEA2079951_01469, SAMEA2079952_01505, SAMEA2079957_01826, SAMEA2079958_01736, SAMEA2079960_01921, SAMEA2079961_01695, SAMEA2079968_01426, SAMEA2080329_01554, SAMEA2080330_01826, SAMEA2080334_01846, SAMEA2080433_01826, SAMEA2080812_01157, SAMEA2080898_01924, SAMEA2080900_01348, SAMEA2080904_01206, SAMEA2080913_01366, SAMEA2081043_01422, SAMEA2081053_01329, SAMEA2081054_00977, SAMEA2081055_01316, SAMEA2081060_01737, SAMEA2081211_00771, SAMEA2081213_01692, SAMEA2081218_01563, SAMEA2081341_01427, SAMEA2081342_01698, SAMEA2081349_01778, SAMEA2081359_01533, SAMEA2081362_01709, SAMEA2081468_01114, SAMEA2081474_01419, SAMEA2081475_01365, SAMEA2081476_00675, SAMEA2081479_01187, SAMEA2081480_01597, SAMEA2081560_01071, SAMEA2081561_01293, SAMEA2081564_01484, SAMEA2081567_01473, SAMEA2081568_01481, SAMEA2081569_01030, SAMEA2081570_01484, SAMEA2081571_01409, SAMEA2081572_01350, SAMEA2081573_01059, SAMEA2081575_01377, SAMEA2081577_01516, SAMEA2081578_01199, SAMEA2081579_01278, SAMEA2081581_01183, SAMEA2081582_01489, SAMEA2081673_01542, SAMEA2081674_01779, SAMEA4008573_01508, SAMEA4008676_01532, SAMEA70146418_01109, SAMEA958766_01227, SAMEA958770_01628, SAMEA958772_01453, SAMEA958778_01291, SAMEA958779_00936, SAMEA958785_01276, SAMEA958793_01651, SAMEA958798_01340, SAMEA958804_01515, SAMEA958810_01295, SAMEA958836_01528, SAMEA958838_01131, SAMEA958845_01585, SAMEA958846_01830, SAMEA958848_01518, SAMEA958855_01764, SAMEA958858_01220, SAMEA958898_00989, SAMEA958906_01622, SAMEA958924_01364, SAMEA958925_01385, SAMEA958951_01382, SAMEA958953_00983, SAMEA958961_00408, SAMEA958979_01232, SAMEA958987_01625, SAMEA958995_01069
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D6HIR7, tRNA (adenine22-N1)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 17% PEG 10,000

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.52→19.4 Å / Num. obs: 36225 / % possible obs: 99.3 % / Redundancy: 2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.034 / Net I/σ(I): 15.6
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 3577 / CC1/2: 0.39

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292115104

Resolution: 1.52→19.37 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.959 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 1986 5.5 %RANDOM
Rwork0.1689 ---
obs0.1724 34239 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.29 Å2 / Biso mean: 17.989 Å2 / Biso min: 8.79 Å2
Baniso -1Baniso -2Baniso -3
1-3.72 Å20 Å20 Å2
2---4.16 Å2-0 Å2
3---0.44 Å2
Refinement stepCycle: final / Resolution: 1.52→19.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 38 273 2078
Biso mean--19.95 35.64 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131916
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171860
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.6322617
X-RAY DIFFRACTIONr_angle_other_deg1.4551.5784292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1945253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95324.554101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27715351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.396159
X-RAY DIFFRACTIONr_chiral_restr0.0940.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022217
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02416
X-RAY DIFFRACTIONr_rigid_bond_restr20.29733776
LS refinement shellResolution: 1.52→1.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 152 -
Rwork0.373 2464 -
all-2616 -
obs--99.35 %

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