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- PDB-5zhm: Crystal structure of TrmD from Pseudomonas aeruginosa in complex ... -

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Basic information

Entry
Database: PDB / ID: 5zhm
TitleCrystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site inhibitor
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / tRNA methyltransferase
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA modification / methylation / cytoplasm
Similarity search - Function
tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases ...tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-9D3 / S-ADENOSYLMETHIONINE / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsZhong, W. / Pasunooti, K.K. / Balamkundu, S. / Wong, Y.W. / Nah, Q. / Liu, C.F. / Lescar, J. / Dedon, P.C.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Singapore SMART Innovation CentreING137070-BIO Singapore
CitationJournal: J.Med.Chem. / Year: 2019
Title: Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-N1)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism.
Authors: Zhong, W. / Pasunooti, K.K. / Balamkundu, S. / Wong, Y.H. / Nah, Q. / Gadi, V. / Gnanakalai, S. / Chionh, Y.H. / McBee, M.E. / Gopal, P. / Lim, S.H. / Olivier, N. / Buurman, E.T. / Dick, T. ...Authors: Zhong, W. / Pasunooti, K.K. / Balamkundu, S. / Wong, Y.H. / Nah, Q. / Gadi, V. / Gnanakalai, S. / Chionh, Y.H. / McBee, M.E. / Gopal, P. / Lim, S.H. / Olivier, N. / Buurman, E.T. / Dick, T. / Liu, C.F. / Lescar, J. / Dedon, P.C.
History
DepositionMar 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Nov 22, 2023Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,4414
Polymers60,6722
Non-polymers7692
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-20 kcal/mol
Surface area21420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.500, 84.500, 147.271
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein tRNA (guanine-N(1)-)-methyltransferase / tRNA [GM37] methyltransferase


Mass: 30336.164 Da / Num. of mol.: 2 / Fragment: UNP residues 5-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: UCBPP-PA14 / Gene: trmD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q02RL6, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-9D3 / N-({4-[(diethylamino)methyl]phenyl}methyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide


Mass: 370.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N4O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris-HCl, pH 8.6-8.8, 20%(v/v) MPD, 20%(w/v) PEG 1000, and 5%(w/v) PEG200; the crystal was soaked with 1mM inhibitor.
PH range: 8.6-8.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.76→49.09 Å / Num. obs: 16240 / % possible obs: 99.9 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 15.2
Reflection shellResolution: 2.76→2.91 Å / Rmerge(I) obs: 0.993 / Num. unique obs: 24471

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WYQ

5wyq


Resolution: 2.76→42.25 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.882 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.375 / SU Rfree Cruickshank DPI: 0.375
RfactorNum. reflection% reflectionSelection details
Rfree0.275 813 5.02 %RANDOM
Rwork0.215 ---
obs0.218 16202 99.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.7127 Å20 Å20 Å2
2---11.7127 Å20 Å2
3---23.4255 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: 1 / Resolution: 2.76→42.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3775 0 53 123 3951
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013917HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.115301HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1401SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes97HARMONIC2
X-RAY DIFFRACTIONt_gen_planes585HARMONIC5
X-RAY DIFFRACTIONt_it3917HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion20.49
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion481SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4557SEMIHARMONIC4
LS refinement shellResolution: 2.76→2.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.334 150 5.22 %
Rwork0.247 2725 -
all0.251 2875 -
obs--99.9 %

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