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- PDB-4zt2: Trypanosoma brucei methionyl-tRNA synthetase in complex with inhi... -

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Basic information

Entry
Database: PDB / ID: 4zt2
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor N-(3,5-dichlorobenzyl)-N'-(1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine (Chem 1575)
ComponentsMethionyl-tRNA synthetaseMethionine—tRNA ligase
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-4RP / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 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)124,22814
Polymers122,8692
Non-polymers1,35912
Water5,855325
1
A: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0818
Polymers61,4351
Non-polymers6467
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1476
Polymers61,4351
Non-polymers7135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.068, 106.070, 207.674
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 / Methionine—tRNA ligase


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, 337 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-4RP / N-(3,5-dichlorobenzyl)-N'-(1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine


Mass: 350.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17Cl2N5
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 3.9 Å3/Da / Density % sol: 68.48 %
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: 2.7→35.35 Å / Num. obs: 53554 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.069 / Net I/σ(I): 10.5 / Num. measured all: 351017
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.7-2.785.80.9411.92586444750.6980.41997.6
11.13-35.356.30.03331.2531184910.01496.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation9.07 Å35.35 Å
Translation9.07 Å-

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Processing

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

4eg8


Resolution: 2.7→35.35 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.919 / Matrix type: sparse / WRfactor Rfree: 0.228 / WRfactor Rwork: 0.194 / SU B: 18.692 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.397 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 2720 5.1 %RANDOM
Rwork0.1943 50766 --
obs0.196 50766 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.98 Å2 / Biso mean: 49.103 Å2 / Biso min: 17.76 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å2-0 Å20 Å2
2---1.41 Å2-0 Å2
3----1.82 Å2
Refinement stepCycle: final / Resolution: 2.7→35.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8330 0 80 325 8735
Biso mean--57.16 37.64 -
Num. residues----1049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198628
X-RAY DIFFRACTIONr_bond_other_d0.0030.028123
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.95511729
X-RAY DIFFRACTIONr_angle_other_deg0.901318659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.44351046
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96123.427391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.154151375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0541556
X-RAY DIFFRACTIONr_chiral_restr0.0620.21303
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219705
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021993
X-RAY DIFFRACTIONr_mcbond_it1.0143.0084196
X-RAY DIFFRACTIONr_mcbond_other1.0143.0074195
X-RAY DIFFRACTIONr_mcangle_it1.7194.5095235
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
2.7-2.770.3272040.2973564388896.9140.297
2.77-2.8450.2991810.2813621380399.9740.281
2.845-2.9270.2721960.254349836941000.254
2.927-3.0170.2621900.233339235821000.233
3.017-3.1150.2531710.229333035011000.229
3.115-3.2230.2841710.214319033611000.214
3.223-3.3440.2461650.202310032651000.202
3.344-3.4790.2151710.207296531361000.207
3.479-3.6320.2291360.197289930351000.197
3.632-3.8070.1971410.192273428751000.192
3.807-4.0110.2241420.177262227641000.177
4.011-4.2510.1961500.163248226321000.163
4.251-4.5390.1891300.152232924591000.152
4.539-4.8960.1831230.149218523081000.149
4.896-5.3530.2251070.173203821451000.173
5.353-5.9680.222850.198187119561000.198
5.968-6.8590.239810.2165517361000.2
6.859-8.3230.189720.179142314951000.179
8.323-11.4570.19650.129114512101000.129
11.457-35.3450.305390.25172276998.960.251
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)
11.8031.1712-1.20263.8548-1.88773.96540.0092-0.3343-0.16290.2227-0.1752-0.30440.04060.30340.1660.0625-0.02970.00640.10720.00960.038911.721-6.77264.293
21.90580.8568-0.93233.5442-0.92642.0184-0.08040.0227-0.0562-0.00890.0709-0.02870.12440.05230.00950.03190.01070.01580.0610.00730.0116-2.109-16.344259.61
35.48420.60290.30514.9644-0.87786.01490.1248-0.2868-1.1060.20610.1047-0.57790.81140.0505-0.22960.19490.0952-0.00350.3030.08290.387228.557-6.114248.921
42.71081.2189-0.72582.7148-0.4162.7777-0.00190.00120.008-0.20980.0461-0.2794-0.33830.4214-0.04420.0805-0.04250.04440.097-0.00110.045225.94513.616239.211
50.566-0.16310.189414.3292-1.91653.17560.2091-0.3920.17040.6392-0.0978-1.7581-0.00280.6181-0.11130.268-0.06230.03280.5074-0.15910.328731.55713.661247.15
62.52060.4983-1.07690.9265-0.47182.5332-0.130.2148-0.1873-0.16760.1007-0.14230.1785-0.04350.02940.0685-0.02410.03120.0679-0.020.033430.36712.17196.868
75.3729-4.43160.78610.5159-0.26543.42460.17810.2838-0.8245-0.0302-0.0038-0.98690.92770.9976-0.17420.35170.085-0.03930.6355-0.09870.532360.70819.97196.2
82.31470.782-1.4592.0103-0.62382.7802-0.0234-0.09690.0354-0.074-0.05330.0386-0.05960.23420.07670.0219-0.01590.01690.0513-0.01420.040837.14822.797203.066
92.29340.4128-0.79052.0954-0.35912.66-0.16450.0631-0.2784-0.1830.0139-0.20690.3915-0.1040.15050.1268-0.01890.04620.05110.00510.052616.229-4.033218.16
1012.041-3.89140.35472.22470.96891.99620.3420.7764-1.5479-0.4707-0.27150.45360.274-0.1361-0.07060.7215-0.06040.01880.34610.05610.29817.299-8.996213.913
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 335
2X-RAY DIFFRACTION2A336 - 546
3X-RAY DIFFRACTION3A547 - 616
4X-RAY DIFFRACTION4A617 - 740
5X-RAY DIFFRACTION5A741 - 767
6X-RAY DIFFRACTION6B-4 - 351
7X-RAY DIFFRACTION7B352 - 403
8X-RAY DIFFRACTION8B404 - 545
9X-RAY DIFFRACTION9B546 - 741
10X-RAY DIFFRACTION10B742 - 767

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