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- PDB-8apu: Crystal Structure of H. influenzae TrmD in complex with Compound 14 -

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Basic information

Entry
Database: PDB / ID: 8apu
TitleCrystal Structure of H. influenzae TrmD in complex with Compound 14
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 / 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
CITRIC ACID / Chem-NMV / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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)30,1983
Polymers29,7501
Non-polymers4482
Water5,134285
1
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)60,3976
Polymers59,5002
Non-polymers8974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area7330 Å2
ΔGint-27 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.607, 94.607, 177.954
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-818-

HOH

21A-867-

HOH

31A-882-

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 (bacteria) / Strain: PittGG / Gene: trmD, CGSHiGG_03625 / Production host: Escherichia coli (E. coli)
References: UniProt: A5UG04, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-NMV / 6-[[4-(aminomethyl)phenyl]methylamino]pyridine-3-carboxamide


Mass: 256.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N4O / 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.: 285 / 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: 53.44 %
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: 1.9→47.348 Å / Num. obs: 24197 / % possible obs: 99.1 % / Redundancy: 10.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.052 / Rrim(I) all: 0.128 / Net I/σ(I): 17.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.33 / Num. unique obs: 1527 / CC1/2: 0.726 / Rpim(I) all: 0.601 / Rrim(I) all: 1.463

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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: 1.9→47.348 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.005 / SU ML: 0.084 / Cross valid method: FREE R-VALUE / ESU R: 0.146 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1933 2453 10.14 %
Rwork0.1742 21738 -
all0.176 --
obs-24191 98.783 %
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: 27.299 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å2-0.001 Å2-0 Å2
2---0.002 Å2-0 Å2
3---0.008 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 32 286 2265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0132027
X-RAY DIFFRACTIONr_bond_other_d0.0020.0151947
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.6432742
X-RAY DIFFRACTIONr_angle_other_deg1.4891.5824489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4965248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34821.524105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10915354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3051516
X-RAY DIFFRACTIONr_chiral_restr0.1010.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022265
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02450
X-RAY DIFFRACTIONr_nbd_refined0.2160.2408
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.21758
X-RAY DIFFRACTIONr_nbtor_refined0.170.2977
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2911
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2880.2194
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.050.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1240.222
X-RAY DIFFRACTIONr_nbd_other0.2360.2113
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2380.239
X-RAY DIFFRACTIONr_mcbond_it2.9832.577992
X-RAY DIFFRACTIONr_mcbond_other2.9762.575991
X-RAY DIFFRACTIONr_mcangle_it4.1693.841237
X-RAY DIFFRACTIONr_mcangle_other4.1673.8441238
X-RAY DIFFRACTIONr_scbond_it4.1922.9791035
X-RAY DIFFRACTIONr_scbond_other4.1822.9751032
X-RAY DIFFRACTIONr_scangle_it5.8814.2881504
X-RAY DIFFRACTIONr_scangle_other5.8794.2891505
X-RAY DIFFRACTIONr_lrange_it7.87732.2622344
X-RAY DIFFRACTIONr_lrange_other7.87632.2742345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.2821920.2641554X-RAY DIFFRACTION97.5419
1.949-2.0030.2651750.241533X-RAY DIFFRACTION97.6558
2.003-2.0610.2311850.2291470X-RAY DIFFRACTION97.8711
2.061-2.1240.2411580.2031461X-RAY DIFFRACTION98.0618
2.124-2.1940.1881350.1821425X-RAY DIFFRACTION98.4227
2.194-2.2710.2031390.1761384X-RAY DIFFRACTION98.5123
2.271-2.3560.2071650.1821311X-RAY DIFFRACTION98.7291
2.356-2.4520.2351320.1781297X-RAY DIFFRACTION98.8927
2.452-2.5610.1861400.161235X-RAY DIFFRACTION99.0634
2.561-2.6860.1491210.1591199X-RAY DIFFRACTION99.2481
2.686-2.8310.1881320.161110X-RAY DIFFRACTION99.2806
2.831-3.0030.1981440.171046X-RAY DIFFRACTION99.5816
3.003-3.210.233990.1681030X-RAY DIFFRACTION99.647
3.21-3.4660.191060.166951X-RAY DIFFRACTION99.8111
3.466-3.7960.153890.157882X-RAY DIFFRACTION99.7944
3.796-4.2430.156830.144801X-RAY DIFFRACTION99.5496
4.243-4.8970.124930.136694X-RAY DIFFRACTION100
4.897-5.9910.182660.169605X-RAY DIFFRACTION100
5.991-8.4450.25590.2477X-RAY DIFFRACTION100
8.445-47.3480.226400.214273X-RAY DIFFRACTION96.3077

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