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- PDB-4zt3: Trypanosoma brucei methionyl-tRNA synthetase in complex with inhi... -

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Basic information

Entry
Database: PDB / ID: 4zt3
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor N-(3,5-dichlorobenzyl)-N'-(5-fluoro-1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine (Chem 1614)
ComponentsMethionyl-tRNA synthetase
KeywordsLigase/Ligase Inhibitor / ligase / aminoacyl-tRNA synthetase / aaRS / MetRS / Trypanosoma brucei / protein-inhibitor complex / 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-4RQ / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsKoh, C.-Y. / Hol, W.G.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Acs Infect Dis. / Year: 2016
Title: 5-Fluoroimidazo[4,5-b]pyridine Is a Privileged Fragment That Conveys Bioavailability to Potent Trypanosomal Methionyl-tRNA Synthetase Inhibitors.
Authors: Zhang, Z. / Koh, C.Y. / Ranade, R.M. / Shibata, S. / Gillespie, J.R. / Hulverson, M.A. / Huang, W. / Nguyen, J. / Pendem, N. / Gelb, M.H. / Verlinde, C.L. / Hol, W.G. / Buckner, F.S. / Fan, E.
History
DepositionMay 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Jan 15, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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
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
B: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,30615
Polymers122,8692
Non-polymers1,43713
Water4,990277
1
A: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0678
Polymers61,4351
Non-polymers6327
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2397
Polymers61,4351
Non-polymers8056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.696, 106.054, 207.453
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


Mass: 61434.707 Da / Num. of mol.: 2 / Fragment: UNP residues 237-773 / Mutation: K456A, K457R, E458A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb10.70.6470 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q38C91, methionine-tRNA ligase

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Non-polymers , 6 types, 290 molecules

#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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-4RQ / N-(3,5-dichlorobenzyl)-N'-(5-fluoro-1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine


Mass: 368.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16Cl2FN5
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 3.88 Å3/Da / Density % sol: 68.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2.0-2.3 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M sodium cacodylate
PH range: 6.0 to 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 20, 2013
RadiationMonochromator: VariMax HF (Osmic) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→38.64 Å / Num. obs: 47919 / % possible obs: 99.9 % / Redundancy: 5.3 % / CC1/2: 0.988 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.094 / Net I/σ(I): 9.8 / Num. measured all: 253141
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.8-2.950.9381.82313946240.5760.465100
10.84-38.644.60.03338418290410.01796.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation9.06 Å38.64 Å
Translation9.06 Å38.64 Å

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHASER2.5.2phasing
REFMACrefmac_5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EG8

4eg8


Resolution: 2.8→38.64 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.892 / Matrix type: sparse / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.209 / SU B: 25.46 / SU ML: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.533 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 2414 5 %RANDOM
Rwork0.209 45441 --
obs0.211 45441 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 154.96 Å2 / Biso mean: 47.767 Å2 / Biso min: 5.63 Å2
Baniso -1Baniso -2Baniso -3
1-4.32 Å2-0 Å20 Å2
2---1.06 Å2-0 Å2
3----3.26 Å2
Refinement stepCycle: final / Resolution: 2.8→38.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8278 0 84 277 8639
Biso mean--59.71 28.25 -
Num. residues----1044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198587
X-RAY DIFFRACTIONr_bond_other_d0.0030.028079
X-RAY DIFFRACTIONr_angle_refined_deg1.0921.95411676
X-RAY DIFFRACTIONr_angle_other_deg0.895318537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.36551043
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54923.308390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.797151358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5541558
X-RAY DIFFRACTIONr_chiral_restr0.0630.21298
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219680
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022000
X-RAY DIFFRACTIONr_mcbond_it0.6022.0624178
X-RAY DIFFRACTIONr_mcbond_other0.6022.0624177
X-RAY DIFFRACTIONr_mcangle_it1.0753.0915213
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2.8-2.8720.3651520.3413290344499.9420.341
2.872-2.9510.3321860.313320433901000.313
2.951-3.0360.3081720.268313833101000.268
3.036-3.1280.3271590.273304532041000.273
3.128-3.230.3181550.259296531201000.259
3.23-3.3430.291620.226284830101000.226
3.343-3.4680.2221510.222277029211000.222
3.468-3.6080.2651260.2212683281099.9640.221
3.608-3.7670.231270.206258227091000.206
3.767-3.9490.2331400.19244125811000.19
3.949-4.1610.2261370.1852328246699.9590.185
4.161-4.410.2021240.1682213234099.8720.168
4.41-4.710.2131230.154207321961000.154
4.71-5.0810.1961040.165198120851000.165
5.081-5.5560.257880.188179918871000.188
5.556-6.1960.249700.202169117611000.202
6.196-7.1240.227790.194146615451000.194
7.124-8.6520.162700.1671270134299.8510.167
8.652-11.9410.201510.1291025107799.9070.129
11.941-38.6390.314380.27762968397.6570.277
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.24362.1896-0.93683.5632-0.88111.07780.045-0.1744-0.26720.2023-0.1462-0.32370.12630.19880.10120.16320.02370.05480.07310.020.101991.8890.73755.195
22.63721.0793-1.25254.5452-1.01543.61140.044-0.04580.07810.043-0.02370.08520.11230.0355-0.02020.0310.01110.04230.00740.02520.117784.81894.63750.495
316.5043-4.7309-5.48631.76971.5371.91521.49811.17720.35350.0486-1.08040.1676-0.6521-0.4753-0.41771.5235-0.59980.08121.64910.03211.5509109.96986.2243.138
45.75271.46170.90523.0566-1.28896.57380.2313-0.4147-1.11750.1426-0.0871-0.86991.21330.1585-0.14420.33190.0954-0.02540.33520.12660.5881115.39698.7541.656
53.33582.0853-1.4444.4091-0.9993.45570.0269-0.1299-0.0367-0.08170.0562-0.52-0.18040.6877-0.08320.0614-0.02820.06250.16-0.02680.1765113.889119.40332.779
62.31040.9485-1.42411.0084-0.77373.9869-0.13930.2668-0.1833-0.27670.1558-0.2457-0.06060.0488-0.01660.2953-0.0850.10650.0699-0.01630.1809116.78118.406-10.937
71.7055-4.6964-0.149813.8766-0.78962.27030.2653-0.025-0.356-0.6775-0.72770.41710.67831.38110.46240.99290.1151-0.10971.11520.02580.9117146.337127.075-10.897
82.80861.5673-1.01912.1999-1.06553.8044-0.017-0.1207-0.1471-0.3080.0262-0.0871-0.16980.4881-0.00920.2752-0.07160.14530.0975-0.0580.269123.751128.355-4.639
92.00740.6312-1.12322.1788-0.25223.5138-0.20690.0793-0.4057-0.25720.0486-0.22490.3707-0.00980.15840.2449-0.00220.05820.01410.00310.1943102.267101.78610.566
1010.2936-4.8877-0.6443.59710.68741.7880.15980.6548-1.1894-0.5374-0.06890.12770.57610.028-0.09090.5373-0.0250.05530.4432-0.04840.511493.83896.966.174
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 414
2X-RAY DIFFRACTION2A415 - 546
3X-RAY DIFFRACTION3A547 - 550
4X-RAY DIFFRACTION4A561 - 612
5X-RAY DIFFRACTION5A613 - 767
6X-RAY DIFFRACTION6B-4 - 351
7X-RAY DIFFRACTION7B352 - 402
8X-RAY DIFFRACTION8B403 - 548
9X-RAY DIFFRACTION9B549 - 741
10X-RAY DIFFRACTION10B742 - 767

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