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- PDB-6swx: Leishmania major methionyl-tRNA synthetase in complex with an all... -

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Basic information

Entry
Database: PDB / ID: 6swx
TitleLeishmania major methionyl-tRNA synthetase in complex with an allosteric inhibitor
ComponentsPutative methionyl-tRNA synthetaseMethionine—tRNA ligase
KeywordsTRANSLATION / LEISHMANIA / PARASITE / AMINOACYL-TRNA SYNTHETASE / TRNA LIGASE / AARS / METRS / METHIONINE / ATP-BINDING / NUCLEOTIDE-BINDING / LIGASE / DRUG DISCOVERY / DUNDEE DRUG DISCOVERY UNIT
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ciliary plasm / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
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 / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Chem-LWN / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRobinson, D.A. / Torrie, L.S. / Shepherd, S.M. / De Rycker, M. / Thomas, M.G. / Wyatt, P.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust204672/Z/16/Z United Kingdom
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Discovery of an Allosteric Binding Site in Kinetoplastid Methionyl-tRNA Synthetase.
Authors: Torrie, L.S. / Robinson, D.A. / Thomas, M.G. / Hobrath, J.V. / Shepherd, S.M. / Post, J.M. / Ko, E.J. / Ferreira, R.A. / Mackenzie, C.J. / Wrobel, K. / Edwards, D.P. / Gilbert, I.H. / Gray, ...Authors: Torrie, L.S. / Robinson, D.A. / Thomas, M.G. / Hobrath, J.V. / Shepherd, S.M. / Post, J.M. / Ko, E.J. / Ferreira, R.A. / Mackenzie, C.J. / Wrobel, K. / Edwards, D.P. / Gilbert, I.H. / Gray, D.W. / Fairlamb, A.H. / De Rycker, M.
History
DepositionSep 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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

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Assembly

Deposited unit
A: Putative methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4823
Polymers63,9851
Non-polymers4982
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area23130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.178, 100.791, 132.056
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative methionyl-tRNA synthetase / Methionine—tRNA ligase


Mass: 63984.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_21_0810 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q4QCD2, methionine-tRNA ligase
#2: Chemical ChemComp-LWN / methyl 2-[[6-[[3,4-bis(fluoranyl)phenyl]amino]-1-methyl-pyrazolo[3,4-d]pyrimidin-4-yl]amino]ethanoate


Mass: 348.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14F2N6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.99 Å3/Da / Density % sol: 58.84 % / Description: Large Cuboid
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 23-28% PEG 3350, 0.2 M K Formate pH 7.0-7.5 / PH range: 7.0 - 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.95→28.55 Å / Num. obs: 53240 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 35 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.037 / Net I/σ(I): 24
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3650 / CC1/2: 0.87 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KFL

3kfl


Resolution: 1.95→28.55 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.128
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2702 5.1 %RANDOM
Rwork0.186 ---
obs0.1874 50467 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 167.72 Å2 / Biso mean: 45.156 Å2 / Biso min: 26.22 Å2
Baniso -1Baniso -2Baniso -3
1-3.19 Å20 Å20 Å2
2---0.38 Å20 Å2
3----2.81 Å2
Refinement stepCycle: final / Resolution: 1.95→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4232 0 34 326 4592
Biso mean--36.36 54.48 -
Num. residues----530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134375
X-RAY DIFFRACTIONr_bond_other_d0.0350.0174016
X-RAY DIFFRACTIONr_angle_refined_deg1.651.645935
X-RAY DIFFRACTIONr_angle_other_deg2.3121.5819309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2325528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96222.658222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74515738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0421522
X-RAY DIFFRACTIONr_chiral_restr0.0810.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024966
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02932
X-RAY DIFFRACTIONr_mcbond_it4.5214.562122
X-RAY DIFFRACTIONr_mcbond_other4.524.562121
X-RAY DIFFRACTIONr_mcangle_it5.7216.8072646
LS refinement shellResolution: 1.954→2.004 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 197 -
Rwork0.309 3658 -
all-3855 -
obs--98.62 %

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