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- PDB-4yvg: Crystal Structure of H. influenzae TrmD in complex with AdoMet -

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Basic information

Entry
Database: PDB / ID: 4yvg
TitleCrystal Structure of H. influenzae TrmD in complex with AdoMet
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / MTase / SPOUT
Function / homology
Function and homology information


tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / 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
S-ADENOSYLMETHIONINE / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.549 Å
AuthorsIto, 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 1.2Aug 19, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1482
Polymers29,7501
Non-polymers3981
Water5,044280
1
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)60,2974
Polymers59,5002
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area7160 Å2
ΔGint-27 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.869, 93.869, 177.952
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

21A-648-

HOH

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Components

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


Mass: 29750.016 Da / Num. of mol.: 1
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: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: sodium citrate, CHES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.549→50 Å / Num. obs: 83679 / % possible obs: 98.4 % / Redundancy: 5.8 % / Net I/σ(I): 31.4

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
HKL-2000data processing
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UAJ

1uaj


Resolution: 1.549→36.806 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2005 1889 4.62 %
Rwork0.174 --
obs0.1752 40917 92.75 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.93 Å2 / ksol: 0.392 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.3371 Å2-0 Å2-0 Å2
2--2.3371 Å2-0 Å2
3----4.6741 Å2
Refinement stepCycle: LAST / Resolution: 1.549→36.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 27 280 2198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021961
X-RAY DIFFRACTIONf_angle_d1.9522656
X-RAY DIFFRACTIONf_dihedral_angle_d15.517742
X-RAY DIFFRACTIONf_chiral_restr0.136292
X-RAY DIFFRACTIONf_plane_restr0.01341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5489-1.59080.21771270.22542671X-RAY DIFFRACTION84
1.5908-1.63760.25321320.22222760X-RAY DIFFRACTION86
1.6376-1.69050.26061380.21312844X-RAY DIFFRACTION88
1.6905-1.75090.24181420.19432810X-RAY DIFFRACTION88
1.7509-1.8210.24581390.19342863X-RAY DIFFRACTION89
1.821-1.90390.23291360.18482843X-RAY DIFFRACTION88
1.9039-2.00420.19141480.17883067X-RAY DIFFRACTION95
2.0042-2.12980.20971530.16743147X-RAY DIFFRACTION98
2.1298-2.29420.19781490.17063128X-RAY DIFFRACTION96
2.2942-2.52510.20971510.17393115X-RAY DIFFRACTION97
2.5251-2.89030.21671540.17713161X-RAY DIFFRACTION97
2.8903-3.6410.18091580.16523267X-RAY DIFFRACTION99
3.641-36.81670.1751620.16113352X-RAY DIFFRACTION99

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