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- PDB-4yvk: Crystal Structure of H. influenzae TrmD in complex with sinefungi... -

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Basic information

Entry
Database: PDB / ID: 4yvk
TitleCrystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA variant (G36C)
Components
  • tRNA
  • tRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE/RNA / MTase / SPOUT / tRNA / TRANSFERASE-RNA complex
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 TrmD / 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 TrmD / 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
SINEFUNGIN / : / RNA / RNA (> 10) / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
Thermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å
AuthorsYoshida, K. / Ito, T. / Yokoyama, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
Authors: Ito, T. / Masuda, I. / Yoshida, K. / Goto-Ito, S. / Sekine, S. / Suh, S.W. / Hou, Y.M. / Yokoyama, S.
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Sep 9, 2015Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 8, 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
C: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0815
Polymers83,3183
Non-polymers7632
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9850 Å2
ΔGint-53 kcal/mol
Surface area31290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.450, 87.450, 228.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein tRNA (guanine-N(1)-)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase


Mass: 29750.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: trmD, HI_0202 / Production host: Escherichia coli (E. coli)
References: UniProt: P43912, tRNA (guanine37-N1)-methyltransferase
#2: RNA chain tRNA


Mass: 23818.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermotoga maritima MSB8 (bacteria) / References: GenBank: 12057205
#3: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: sodium acetate trihydrate, ammonium phosphate monobasic, PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 18509 / % possible obs: 99.8 % / Redundancy: 7.3 % / Net I/σ(I): 20.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data processing
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YVI

4yvi


Resolution: 3.002→43.725 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2832 945 5.12 %
Rwork0.2185 --
obs0.2218 18457 99.6 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.418 Å2 / ksol: 0.299 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1667 Å2-0 Å2-0 Å2
2---0.1667 Å20 Å2
3---0.3334 Å2
Refinement stepCycle: LAST / Resolution: 3.002→43.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3846 1516 54 0 5416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0185897
X-RAY DIFFRACTIONf_angle_d1.3348037
X-RAY DIFFRACTIONf_dihedral_angle_d16.8842352
X-RAY DIFFRACTIONf_chiral_restr0.078948
X-RAY DIFFRACTIONf_plane_restr0.007767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0024-3.16060.36491330.28922373X-RAY DIFFRACTION98
3.1606-3.35860.30261440.23752453X-RAY DIFFRACTION100
3.3586-3.61780.3041300.23222454X-RAY DIFFRACTION100
3.6178-3.98160.30211190.21222510X-RAY DIFFRACTION100
3.9816-4.55730.26111480.20012477X-RAY DIFFRACTION100
4.5573-5.73960.2741430.20732536X-RAY DIFFRACTION100
5.7396-43.72960.27181280.21882709X-RAY DIFFRACTION100

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