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- PDB-8apt: Crystal Structure of H. influenzae TrmD in complex with Compound 13 -

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Basic information

Entry
Database: PDB / ID: 8apt
TitleCrystal Structure of H. influenzae TrmD in complex with Compound 13
ComponentstRNA (guanine-N(1)-)-methyltransferaseTRNA (guanine9-N1)-methyltransferase
KeywordsRNA BINDING PROTEIN / Methyltransferase
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA modification / methylation / cytoplasm
Similarity search - Function
tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
CITRIC ACID / Chem-NN9 / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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
Water7,494416
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 area7500 Å2
ΔGint-29 kcal/mol
Surface area22920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.671, 94.671, 177.958
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-615-

HOH

21A-654-

HOH

31A-742-

HOH

41A-773-

HOH

51A-794-

HOH

61A-812-

HOH

71A-816-

HOH

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Components

#1: Protein tRNA (guanine-N(1)-)-methyltransferase / TRNA (guanine9-N1)-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-NN9 / 6-[[3-(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 / Citric acid


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


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
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: 1.8→47.38 Å / Num. obs: 28700 / % possible obs: 99.8 % / Redundancy: 10.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.075 / Rrim(I) all: 0.174 / Net I/σ(I): 14.9
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.186 / Num. unique obs: 1639 / CC1/2: 0.559 / Rpim(I) all: 0.643 / Rrim(I) all: 1.357

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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: 1.8→47.38 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.287 / SU ML: 0.069 / Cross valid method: FREE R-VALUE / ESU R: 0.116 / ESU R Free: 0.102
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1794 2931 10.213 %
Rwork0.1613 25767 -
all0.163 --
obs-28698 99.805 %
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: 18.697 Å2
Baniso -1Baniso -2Baniso -3
1-0.002 Å20.001 Å20 Å2
2--0.002 Å20 Å2
3----0.006 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 32 416 2395
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_deg1.8471.6432742
X-RAY DIFFRACTIONr_angle_other_deg1.5211.5824489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5345248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57721.524105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01915354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9951516
X-RAY DIFFRACTIONr_chiral_restr0.1080.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022265
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02450
X-RAY DIFFRACTIONr_nbd_refined0.2310.2424
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.21785
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2972
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2921
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.330.2302
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.090.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.225
X-RAY DIFFRACTIONr_nbd_other0.2520.2111
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4120.255
X-RAY DIFFRACTIONr_mcbond_it2.1581.62992
X-RAY DIFFRACTIONr_mcbond_other2.1471.618991
X-RAY DIFFRACTIONr_mcangle_it2.9312.4161237
X-RAY DIFFRACTIONr_mcangle_other2.9312.4191238
X-RAY DIFFRACTIONr_scbond_it3.3381.9331035
X-RAY DIFFRACTIONr_scbond_other3.3191.9291032
X-RAY DIFFRACTIONr_scangle_it4.8992.7571504
X-RAY DIFFRACTIONr_scangle_other4.8972.7591505
X-RAY DIFFRACTIONr_lrange_it11.21822.8762466
X-RAY DIFFRACTIONr_lrange_other10.66720.8552299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.2942050.2831830X-RAY DIFFRACTION97.6956
1.847-1.8970.2541830.2311868X-RAY DIFFRACTION99.9513
1.897-1.9520.2142200.2081776X-RAY DIFFRACTION100
1.952-2.0120.1992130.1821742X-RAY DIFFRACTION100
2.012-2.0780.2122140.181650X-RAY DIFFRACTION100
2.078-2.1510.1881480.1621669X-RAY DIFFRACTION100
2.151-2.2320.1651830.1531576X-RAY DIFFRACTION100
2.232-2.3230.1631730.1491497X-RAY DIFFRACTION100
2.323-2.4270.1781910.1451455X-RAY DIFFRACTION100
2.427-2.5450.1511600.1471391X-RAY DIFFRACTION100
2.545-2.6820.1591610.1471321X-RAY DIFFRACTION100
2.682-2.8450.171390.1461273X-RAY DIFFRACTION100
2.845-3.0410.1781390.1581183X-RAY DIFFRACTION100
3.041-3.2840.1651200.1551124X-RAY DIFFRACTION100
3.284-3.5970.1581020.1491037X-RAY DIFFRACTION100
3.597-4.020.1571220.131922X-RAY DIFFRACTION100
4.02-4.640.175790.13840X-RAY DIFFRACTION100
4.64-5.6770.148850.14714X-RAY DIFFRACTION100
5.677-8.0060.262640.195554X-RAY DIFFRACTION100
8.006-47.380.151300.194345X-RAY DIFFRACTION98.1675

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