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- PDB-5zhi: Apo crystal structure of TrmD from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 5zhi
TitleApo crystal structure of TrmD from Mycobacterium tuberculosis
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 N1-guanine methylation / cytosol
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
tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.3Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)52,3412
Polymers52,3412
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-26 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.170, 113.070, 44.210
Angle α, β, γ (deg.)90.00, 110.75, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 226 / Label seq-ID: 1 - 226

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 26170.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: trmD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P9WFY6, tRNA (guanine37-N1)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 1.97 Å3/Da / Density % sol: 37.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM Bis-Tris at pH 6.5, 20%(w/v) PEG3350, 0.1M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.544
11-L, -K, -H20.456
ReflectionResolution: 2.2→41.3 Å / Num. obs: 19717 / % possible obs: 96.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.1
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.226 / Num. unique obs: 5534 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology modeling from I-TASSER server

Resolution: 2.2→38.83 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.622 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.041 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2001 983 5 %RANDOM
Rwork0.15958 ---
obs0.16159 18708 95.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.463 Å2
Baniso -1Baniso -2Baniso -3
1--7.73 Å20 Å2-3.03 Å2
2--13.05 Å20 Å2
3----5.32 Å2
Refinement stepCycle: 1 / Resolution: 2.2→38.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3245 0 0 87 3332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193322
X-RAY DIFFRACTIONr_bond_other_d0.0010.023152
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9634521
X-RAY DIFFRACTIONr_angle_other_deg0.76237248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3765418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24922.109147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30315536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5441540
X-RAY DIFFRACTIONr_chiral_restr0.0870.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213706
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02698
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8991.8811681
X-RAY DIFFRACTIONr_mcbond_other1.8961.8811680
X-RAY DIFFRACTIONr_mcangle_it2.9292.8062096
X-RAY DIFFRACTIONr_mcangle_other2.9282.8072097
X-RAY DIFFRACTIONr_scbond_it2.0172.081641
X-RAY DIFFRACTIONr_scbond_other2.0162.0811642
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1573.0432426
X-RAY DIFFRACTIONr_long_range_B_refined5.71834.90613026
X-RAY DIFFRACTIONr_long_range_B_other5.70734.91313008
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12306 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 65 -
Rwork0.167 1249 -
obs--88.72 %

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