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- PDB-5nfh: Trypanosoma brucei methionyl-tRNA synthetase in complex with a qu... -

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Basic information

Entry
Database: PDB / ID: 5nfh
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with a quinazolinone inhibitor
ComponentsMethionyl-tRNA synthetase, putative
KeywordsLIGASE / SYNTHETASE / METHIONINE / INHIBITOR / LIGASE-LIGASE INHIBITOR / COMPLEX / DRUG DISCOVERY
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ciliary plasm / ATP binding / cytoplasm
Similarity search - Function
Methionyl-trna Synthetase; domain 2 / Methionyl-trna Synthetase; domain 2 - #10 / Methionine-tRNA synthetase, type 2 / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / Methionyl/Leucyl tRNA synthetase ...Methionyl-trna Synthetase; domain 2 / Methionyl-trna Synthetase; domain 2 - #10 / Methionine-tRNA synthetase, type 2 / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-8W2 / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsRobinson, D.A. / Eadsforth, T.C. / Shepherd, S.M. / Torrie, L.S. / De Rycker, M. / Gilbert, I.H.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust092340 United Kingdom
Wellcome Trust105021 United Kingdom
Wellcome Trust100476 United Kingdom
CitationJournal: ACS Infect Dis / Year: 2017
Title: Chemical Validation of Methionyl-tRNA Synthetase as a Druggable Target in Leishmania donovani.
Authors: Torrie, L.S. / Brand, S. / Robinson, D.A. / Ko, E.J. / Stojanovski, L. / Simeons, F.R.C. / Wyllie, S. / Thomas, J. / Ellis, L. / Osuna-Cabello, M. / Epemolu, O. / Nuhs, A. / Riley, J. / ...Authors: Torrie, L.S. / Brand, S. / Robinson, D.A. / Ko, E.J. / Stojanovski, L. / Simeons, F.R.C. / Wyllie, S. / Thomas, J. / Ellis, L. / Osuna-Cabello, M. / Epemolu, O. / Nuhs, A. / Riley, J. / MacLean, L. / Manthri, S. / Read, K.D. / Gilbert, I.H. / Fairlamb, A.H. / De Rycker, M.
History
DepositionMar 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionyl-tRNA synthetase, putative
B: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,59812
Polymers121,3382
Non-polymers1,26010
Water4,738263
1
A: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3438
Polymers60,6691
Non-polymers6747
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2564
Polymers60,6691
Non-polymers5873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.090, 105.985, 207.071
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Methionyl-tRNA synthetase, putative


Mass: 60669.031 Da / Num. of mol.: 2 / Mutation: K452A, K453R, E454A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb10.70.6470 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38C91, methionine-tRNA ligase

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Non-polymers , 5 types, 273 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#5: Chemical ChemComp-8W2 / 2-[3-[[4,6-bis(chloranyl)-1~{H}-indol-2-yl]methylamino]propylamino]-3~{H}-quinazolin-4-one


Mass: 416.304 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19Cl2N5O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 3.93 Å3/Da / Density % sol: 68.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 2.0-2.3 M Ammonium Sulphate, 0.2 M NaCl, 0.1 M Na Cacodylate pH 6.4
PH range: 6.0-6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2014
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 47875 / % possible obs: 99.8 % / Redundancy: 4.6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.082 / Rrim(I) all: 0.176 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.8-2.94.50.8060.6830.4130.90999.9
10.84-5040.0370.9980.0210.04298.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.2.7data scaling
REFMACrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EGA

4ega


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 12.895 / SU ML: 0.24 / SU R Cruickshank DPI: 0.5035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.504 / ESU R Free: 0.288
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 2417 5.1 %RANDOM
Rwork0.1948 ---
obs0.1966 45397 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 162.18 Å2 / Biso mean: 45.056 Å2 / Biso min: 10.18 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å20 Å2
2--0.89 Å20 Å2
3----2.91 Å2
Refinement stepCycle: final / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8346 0 79 263 8688
Biso mean--55.74 37.39 -
Num. residues----1046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198652
X-RAY DIFFRACTIONr_bond_other_d0.0010.028181
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.96111756
X-RAY DIFFRACTIONr_angle_other_deg2.2183.00118816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7351045
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12623.46396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.451151411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.371557
X-RAY DIFFRACTIONr_chiral_restr0.0630.21295
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219651
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022001
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 172 -
Rwork0.321 3281 -
all-3453 -
obs--99.86 %

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