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- PDB-5j59: Trypanosoma brucei methionyl-tRNA synthetase in complex with inhi... -

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Basic information

Entry
Database: PDB / ID: 5j59
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (Chem 1893)
ComponentsMethionyl-tRNA synthetase, putative
KeywordsLigase/Ligase Inhibitor / synthetase / ligase / methionine / inhibitor / Ligase-Ligase Inhibitor complex
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
METHIONINE / Chem-N93 / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBarros-Alvarez, X. / Hol, W.G.J.
CitationJournal: Eur J Med Chem / Year: 2016
Title: Structure-guided design of novel Trypanosoma brucei Methionyl-tRNA synthetase inhibitors.
Authors: Huang, W. / Zhang, Z. / Barros-Alvarez, X. / Koh, C.Y. / Ranade, R.M. / Gillespie, J.R. / Creason, S.A. / Shibata, S. / Verlinde, C.L. / Hol, W.G. / Buckner, F.S. / Fan, E.
History
DepositionApr 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)123,2875
Polymers122,6612
Non-polymers6263
Water8,269459
1
A: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4802
Polymers61,3311
Non-polymers1491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8083
Polymers61,3311
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.310, 106.400, 207.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 238 - 766 / Label seq-ID: 7 - 535

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Methionyl-tRNA synthetase, putative


Mass: 61330.715 Da / Num. of mol.: 2 / Mutation: A309T, K452A, K453R, E454A, A499V, S503N
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
#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-N93 / 5-chloro-N-(2-{[(3,5-dichlorophenyl)methyl]amino}ethyl)-N-methyl-3H-imidazo[4,5-b]pyridin-2-amine


Mass: 384.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16Cl3N5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 3.94 Å3/Da / Density % sol: 68.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1.8-2.1 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M sodium cacodylate, pH 6.2-6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2015
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→103.96 Å / Num. obs: 75745 / % possible obs: 99.2 % / Redundancy: 12.4 % / Net I/σ(I): 8.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimlessdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→103.96 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20745 3708 4.9 %RANDOM
Rwork0.19166 ---
obs0.19245 71736 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.817 Å2
Baniso -1Baniso -2Baniso -3
1-3.41 Å2-0 Å20 Å2
2---1.88 Å2-0 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 2.4→103.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8302 0 39 459 8800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198577
X-RAY DIFFRACTIONr_bond_other_d00.028047
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.94911673
X-RAY DIFFRACTIONr_angle_other_deg3.694318487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57651049
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17423.463387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.983151367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3691554
X-RAY DIFFRACTIONr_chiral_restr0.0710.21290
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219713
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021995
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0414.8174206
X-RAY DIFFRACTIONr_mcbond_other2.0414.8174207
X-RAY DIFFRACTIONr_mcangle_it3.437.2125248
X-RAY DIFFRACTIONr_mcangle_other3.4297.2125249
X-RAY DIFFRACTIONr_scbond_it2.4595.0424371
X-RAY DIFFRACTIONr_scbond_other2.4595.0424372
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1497.456424
X-RAY DIFFRACTIONr_long_range_B_refined7.54138.719912
X-RAY DIFFRACTIONr_long_range_B_other7.54238.7059910
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 60206 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 261 -
Rwork0.265 5238 -
obs--98.21 %

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