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- PDB-4mcd: hinTrmD in complex with 5-PHENYLTHIENO[2,3-D]PYRIMIDIN-4(3H)-ONE -

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Basic information

Entry
Database: PDB / ID: 4mcd
TitlehinTrmD in complex with 5-PHENYLTHIENO[2,3-D]PYRIMIDIN-4(3H)-ONE
ComponentstRNA (guanine-N(1)-)-methyltransferaseTRNA (guanine9-N1)-methyltransferase
Keywordstransferase/transferase inhibitor / trefoil / TrmD / SAM / SAH / Sinefungin / HMT / Structural Genomics / transferase-transferase inhibitor complex
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
5-phenylthieno[2,3-d]pyrimidin-4(3H)-one / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae Rd KW20 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLahiri, S.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Selective Inhibitors of Bacterial t-RNA-(N(1)G37) Methyltransferase (TrmD) That Demonstrate Novel Ordering of the Lid Domain.
Authors: Hill, P.J. / Abibi, A. / Albert, R. / Andrews, B. / Gagnon, M.M. / Gao, N. / Grebe, T. / Hajec, L.I. / Huang, J. / Livchak, S. / Lahiri, S.D. / McKinney, D.C. / Thresher, J. / Wang, H. / ...Authors: Hill, P.J. / Abibi, A. / Albert, R. / Andrews, B. / Gagnon, M.M. / Gao, N. / Grebe, T. / Hajec, L.I. / Huang, J. / Livchak, S. / Lahiri, S.D. / McKinney, D.C. / Thresher, J. / Wang, H. / Olivier, N. / Buurman, E.T.
History
DepositionAug 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,8072
Polymers27,5791
Non-polymers2281
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)55,6144
Polymers55,1572
Non-polymers4572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area7070 Å2
ΔGint-26 kcal/mol
Surface area21110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.345, 93.345, 178.908
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-470-

HOH

21A-496-

HOH

31A-524-

HOH

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Components

#1: Protein tRNA (guanine-N(1)-)-methyltransferase / TRNA (guanine9-N1)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase


Mass: 27578.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Tet r.
Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria)
Strain: ATCC51907 / Gene: HI_0202, trmD / Plasmid: pET system / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3
References: UniProt: P43912, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-22L / 5-phenylthieno[2,3-d]pyrimidin-4(3H)-one


Mass: 228.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8N2OS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Protein at 10 mg/mL in the buffer: 20mM Tris pH 8.0, 150 mM NaCl, 10% Glycerol, 1mM DTT, 1mM EDTA. mixed 1:1 with well solution containing: 200 mM CaAcetate, 24% PEG 400, 100 mM Sodium ...Details: Protein at 10 mg/mL in the buffer: 20mM Tris pH 8.0, 150 mM NaCl, 10% Glycerol, 1mM DTT, 1mM EDTA. mixed 1:1 with well solution containing: 200 mM CaAcetate, 24% PEG 400, 100 mM Sodium Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97 Å
DetectorDetector: CCD / Date: Feb 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.287→30.124 Å / Num. obs: 43053 / % possible obs: 98.6 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.186 / Rsym value: 0.186 / Net I/σ(I): 6.3
Reflection shell

Rmerge(I) obs: 0.032 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.55-1.638.10.24865059953.22595.1
1.63-1.7310.60.36231759032.63898.7
1.73-1.8510.60.55866855461.63298.9
1.85-210.60.95509251990.8399.1
2-2.1910.61.85112748210.42399.4
2.19-2.4510.634651243720.25499.4
2.45-2.8310.64.54117238710.16499.7
2.83-3.4710.653498833040.12599.8
3.47-4.910.58.52719725970.07399.9
4.9-30.1249.9151426714450.04297.5

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Processing

Software
NameVersionClassificationNB
SCALA3.2.5data scaling
REFMAC5.5.0046refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
d*TREKdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→30.12 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.947 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 2113 5.1 %RANDOM
Rwork0.2053 ---
obs0.2068 41769 95.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 69.86 Å2 / Biso mean: 28.122 Å2 / Biso min: 11.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20.52 Å20 Å2
2--1.03 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 16 206 2094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221930
X-RAY DIFFRACTIONr_bond_other_d0.0010.021332
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.9832611
X-RAY DIFFRACTIONr_angle_other_deg0.84933243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1415235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94823.72186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28315341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5071515
X-RAY DIFFRACTIONr_chiral_restr0.0720.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02376
X-RAY DIFFRACTIONr_mcbond_it0.7461.51174
X-RAY DIFFRACTIONr_mcbond_other0.1641.5482
X-RAY DIFFRACTIONr_mcangle_it1.44221888
X-RAY DIFFRACTIONr_scbond_it2.1783756
X-RAY DIFFRACTIONr_scangle_it3.7274.5723
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 99 -
Rwork0.402 1983 -
all-2082 -
obs--65.57 %
Refinement TLS params.Method: refined / Origin x: 29.0803 Å / Origin y: 69.7257 Å / Origin z: 59.7586 Å
111213212223313233
T0.0119 Å2-0.003 Å2-0.0017 Å2-0.0038 Å2-0.0037 Å2--0.0312 Å2
L0.1005 °2-0.0975 °20.1277 °2-0.2882 °2-0.4188 °2--0.8929 °2
S-0.0176 Å °-0.0075 Å °0.0097 Å °0.0054 Å °0.0005 Å °-0.0284 Å °-0.0509 Å °0.0289 Å °0.0172 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A401 - 606
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A1 - 246

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