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- PDB-5tqu: Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 5tqu
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor
ComponentsMethionyl-tRNA synthetase, putativeMethionine—tRNA ligase
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
Chem-I53 / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBarros-Alvarez, X. / Hol, W.G.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1 AI084004 and RO1 AI097177 United States
CitationJournal: ACS Infect Dis / Year: 2017
Title: From Cells to Mice to Target: Characterization of NEU-1053 (SB-443342) and Its Analogues for Treatment of Human African Trypanosomiasis.
Authors: Devine, W.G. / Diaz-Gonzalez, R. / Ceballos-Perez, G. / Rojas, D. / Satoh, T. / Tear, W. / Ranade, R.M. / Barros-Alvarez, X. / Hol, W.G. / Buckner, F.S. / Navarro, M. / Pollastri, M.P.
History
DepositionOct 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.name
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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 / 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)123,4316
Polymers122,6612
Non-polymers7704
Water3,693205
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
2
B: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9514
Polymers61,3311
Non-polymers6213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-26 kcal/mol
Surface area40520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.960, 106.320, 207.590
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: 0 / 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: 0 / Auth seq-ID: 238 - 766 / Label seq-ID: 7 - 535

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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Methionyl-tRNA synthetase, putative / Methionine—tRNA ligase


Mass: 61330.715 Da / Num. of mol.: 2
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, 209 molecules

#2: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical ChemComp-I53 / 2-[2-[[3-(1~{H}-benzimidazol-2-ylamino)propylamino]methyl]-4,6-bis(chloranyl)indol-1-yl]ethanol


Mass: 432.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23Cl2N5O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 3.96 Å3/Da / Density % sol: 68.91 %
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: 2.6→103.79 Å / Num. obs: 60480 / % possible obs: 99.7 % / Redundancy: 5.9 % / Net I/σ(I): 5.5
Reflection shellResolution: 2.6→2.67 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimlessdata scaling
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MW0

4mw0


Resolution: 2.6→103.79 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / ESU R: 0.332 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24122 2965 4.9 %RANDOM
Rwork0.21284 ---
obs0.21423 57423 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.214 Å2
Baniso -1Baniso -2Baniso -3
1-5.67 Å2-0 Å20 Å2
2---3.01 Å2-0 Å2
3----2.67 Å2
Refinement stepCycle: 1 / Resolution: 2.6→103.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8089 0 49 205 8343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198356
X-RAY DIFFRACTIONr_bond_other_d00.027838
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.95111374
X-RAY DIFFRACTIONr_angle_other_deg3.686317994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68451024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3923.369374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26151322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7421554
X-RAY DIFFRACTIONr_chiral_restr0.0750.21260
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219502
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021942
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_it3.3496.034106
X-RAY DIFFRACTIONr_mcbond_other3.3486.034105
X-RAY DIFFRACTIONr_mcangle_it5.3759.0345124
X-RAY DIFFRACTIONr_mcangle_other5.3759.0345125
X-RAY DIFFRACTIONr_scbond_it3.6676.2554250
X-RAY DIFFRACTIONr_scbond_other3.6656.2554246
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9639.266244
X-RAY DIFFRACTIONr_long_range_B_refined8.58447.7219509
X-RAY DIFFRACTIONr_long_range_B_other8.58447.7229509
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 57906 / 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: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 205 -
Rwork0.377 4136 -
obs--98.12 %

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