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- PDB-8apv: Crystal Structure of H. influenzae TrmD in complex with Compound 27 -

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Basic information

Entry
Database: PDB / ID: 8apv
TitleCrystal Structure of H. influenzae TrmD in complex with Compound 27
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsRNA BINDING PROTEIN / 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 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
CITRIC ACID / Chem-NLL / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHall, G. / Cowan, R. / Carr, M.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other government United Kingdom
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2023
Title: Evaluating the druggability of TrmD, a potential antibacterial target, through design and microbiological profiling of a series of potent TrmD inhibitors.
Authors: Wilkinson, A.J. / Ooi, N. / Finlayson, J. / Lee, V.E. / Lyth, D. / Maskew, K.S. / Newman, R. / Orr, D. / Ansell, K. / Birchall, K. / Canning, P. / Coombs, P. / Fusani, L. / McIver, E. / ...Authors: Wilkinson, A.J. / Ooi, N. / Finlayson, J. / Lee, V.E. / Lyth, D. / Maskew, K.S. / Newman, R. / Orr, D. / Ansell, K. / Birchall, K. / Canning, P. / Coombs, P. / Fusani, L. / McIver, E. / Pisco, J. / Ireland, P.M. / Jenkins, C. / Norville, I.H. / Southern, S.J. / Cowan, R. / Hall, G. / Kettleborough, C. / Savage, V.J. / Cooper, I.R.
History
DepositionAug 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2223
Polymers29,7501
Non-polymers4722
Water1,69394
1
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)60,4456
Polymers59,5002
Non-polymers9454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area7250 Å2
ΔGint-29 kcal/mol
Surface area22980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.630, 94.630, 178.015
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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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 (bacteria) / Strain: PittGG / Gene: trmD, CGSHiGG_03625 / Production host: Escherichia coli (E. coli)
References: UniProt: A5UG04, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-NLL / 1-[[4-(aminomethyl)phenyl]methyl]pyrrolo[2,3-b]pyridine-5-carboxamide


Mass: 280.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350 0.1 M HEPES, pH 7.5 0.1 M potassium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→47.36 Å / Num. obs: 12287 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.102 / Rrim(I) all: 0.199 / Net I/σ(I): 11.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.929 / Num. unique obs: 1275 / CC1/2: 0.696 / Rpim(I) all: 0.624 / Rrim(I) all: 1.124

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
StructureStudiodata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YVH

4yvh


Resolution: 2.4→47.36 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.896 / SU B: 7.446 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / ESU R: 0.34 / ESU R Free: 0.26
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2526 588 4.786 %
Rwork0.1777 11699 -
all0.181 --
obs-12287 99.886 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.104 Å20.052 Å20 Å2
2--0.104 Å20 Å2
3----0.339 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 34 94 2075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132030
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151947
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.6432748
X-RAY DIFFRACTIONr_angle_other_deg1.3921.5824489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4315248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.421.524105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29515354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0311516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022265
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
X-RAY DIFFRACTIONr_nbd_refined0.2160.2405
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.21816
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2975
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21055
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.280
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.120.225
X-RAY DIFFRACTIONr_nbd_other0.2190.2114
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4450.219
X-RAY DIFFRACTIONr_mcbond_it3.4792.943992
X-RAY DIFFRACTIONr_mcbond_other3.4712.941991
X-RAY DIFFRACTIONr_mcangle_it5.1434.3961237
X-RAY DIFFRACTIONr_mcangle_other5.1444.41238
X-RAY DIFFRACTIONr_scbond_it3.913.2891038
X-RAY DIFFRACTIONr_scbond_other3.9083.2851035
X-RAY DIFFRACTIONr_scangle_it5.8644.7571510
X-RAY DIFFRACTIONr_scangle_other5.8624.761511
X-RAY DIFFRACTIONr_lrange_it7.63933.2672239
X-RAY DIFFRACTIONr_lrange_other7.63433.2372232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.303380.21844X-RAY DIFFRACTION99.7738
2.462-2.530.284390.206844X-RAY DIFFRACTION100
2.53-2.6030.259410.199819X-RAY DIFFRACTION100
2.603-2.6830.344400.202763X-RAY DIFFRACTION100
2.683-2.7710.339320.214781X-RAY DIFFRACTION100
2.771-2.8680.281390.189733X-RAY DIFFRACTION100
2.868-2.9760.21450.19701X-RAY DIFFRACTION100
2.976-3.0970.266350.189690X-RAY DIFFRACTION100
3.097-3.2350.228350.186661X-RAY DIFFRACTION100
3.235-3.3930.275340.194626X-RAY DIFFRACTION100
3.393-3.5760.274270.189592X-RAY DIFFRACTION100
3.576-3.7920.208270.155593X-RAY DIFFRACTION100
3.792-4.0530.202340.156530X-RAY DIFFRACTION100
4.053-4.3770.2260.151498X-RAY DIFFRACTION100
4.377-4.7930.223220.139481X-RAY DIFFRACTION99.8016
4.793-5.3560.191160.133423X-RAY DIFFRACTION99.5465
5.356-6.1790.256180.181378X-RAY DIFFRACTION100
6.179-7.5550.276190.194323X-RAY DIFFRACTION100
7.555-10.6290.14100.141264X-RAY DIFFRACTION100
10.629-47.360.612110.245155X-RAY DIFFRACTION96.5116

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