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- PDB-4mcc: HinTrmD in complex with N-[4-(AMINOMETHYL)BENZYL]-4-OXO-3,4-DIHYD... -

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Basic information

Entry
Database: PDB / ID: 4mcc
TitleHinTrmD in complex with N-[4-(AMINOMETHYL)BENZYL]-4-OXO-3,4-DIHYDROTHIENO[2,3-D]PYRIMIDINE-5-CARBOXAMIDE
ComponentstRNA (guanine-N(1)-)-methyltransferase
Keywordstransferase/transferase inhibitor / trefoil / TrmD / SAM / SAH / Sinefungin / HMT / Structural Genomics / N/A / 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
Chem-21X / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsOlivier, N.B. / Hill, P.
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 4, 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
B: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7864
Polymers55,1572
Non-polymers6292
Water7,422412
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-26 kcal/mol
Surface area20420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.272, 74.272, 119.135
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 27578.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (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-21X / N-[4-(aminomethyl)benzyl]-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide


Mass: 314.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H14N4O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.98 Å3/Da / Density % sol: 58.71 %
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
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 10, 2012
Details: Source: 3.3 Undulator (Undulator A) Monochromator Type: Diamond(111) Energy Range 4.7-28 keV Resolution ( E/E) 1 x 10 -4 Flux (photons/sec) 2 x 1012 @12.4 keV Beam Size (HxV) Focused 80 m x 70 m
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.949→119.135 Å / Num. all: 47060 / Num. obs: 47060 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 30.9 Å2 / Rsym value: 0.057 / Net I/σ(I): 21.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-2.057.50.4621.65154268440.462100
2.05-2.187.60.2952.64913964810.295100
2.18-2.337.60.18844636061060.188100
2.33-2.527.60.135.84327056770.13100
2.52-2.767.60.0858.83992252410.085100
2.76-3.087.60.06211.93586947160.062100
3.08-3.567.50.04415.23156541860.044100
3.56-4.367.40.03419.22640135460.034100
4.36-6.167.50.02922.12065727520.029100
6.16-119.1357.10.02327.11074815110.02398.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.11data extraction
SPECdata collection
PROCESSdata reduction
AMoREphasing
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.66 Å / Cor.coef. Fo:Fc: 0.9505 / Cor.coef. Fo:Fc free: 0.9384 / Occupancy max: 1 / Occupancy min: 0.32 / SU R Cruickshank DPI: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 2376 5.07 %RANDOM
Rwork0.1811 ---
obs0.1824 46878 99.96 %-
Displacement parametersBiso max: 136.68 Å2 / Biso mean: 36.776 Å2 / Biso min: 16.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.258 Å20 Å20 Å2
2---1.258 Å20 Å2
3---2.516 Å2
Refine analyzeLuzzati coordinate error obs: 0.194 Å
Refinement stepCycle: LAST / Resolution: 1.95→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 44 412 3874
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1234SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes526HARMONIC5
X-RAY DIFFRACTIONt_it3547HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion447SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4275SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3547HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4805HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion16.96
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2218 185 5.38 %
Rwork0.1864 3254 -
all0.1883 3439 -
obs--99.96 %

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