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- PDB-4zt5: Trypanosoma brucei methionyl-tRNA synthetase in complex with inhi... -

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Basic information

Entry
Database: PDB / ID: 4zt5
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (2S)-N-(3,5-dichlorobenzyl)-N'-(1H-imidazo[4,5-b]pyridin-2-yl)-2-methylpropane-1,3-diamine (Chem 1655)
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-4RN / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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 / diffrn_radiation_wavelength / 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)124,22414
Polymers122,8692
Non-polymers1,35512
Water7,999444
1
A: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9897
Polymers61,4351
Non-polymers5546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2357
Polymers61,4351
Non-polymers8016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.794, 106.021, 207.659
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, 456 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 364.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19Cl2N5
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 3.89 Å3/Da / Density % sol: 68.36 %
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: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 23, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.35→39.43 Å / Num. obs: 80610 / % possible obs: 100 % / Redundancy: 15 % / CC1/2: 0.999 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.046 / Net I/σ(I): 17.5 / Num. measured all: 1208827 / Scaling rejects: 1
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
2.35-2.415.11.881.86881545430.6890.496100
11.98-39.4312.70.02670.4880569410.00797.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.7 Å38.67 Å
Translation8.7 Å38.67 Å

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Processing

Software
NameVersionClassification
Aimless0.2.14data scaling
PHASER2.5.5phasing
REFMACrefmac_5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EG8

4eg8


Resolution: 2.35→38.67 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / Matrix type: sparse / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.2 / SU B: 14.053 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 4035 5 %RANDOM
Rwork0.2001 76494 --
obs0.2016 76494 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.16 Å2 / Biso mean: 51.265 Å2 / Biso min: 26.54 Å2
Baniso -1Baniso -2Baniso -3
1-7.16 Å2-0 Å20 Å2
2---2.74 Å2-0 Å2
3----4.42 Å2
Refinement stepCycle: final / Resolution: 2.35→38.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8259 0 80 444 8783
Biso mean--68.05 48.79 -
Num. residues----1049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198548
X-RAY DIFFRACTIONr_bond_other_d0.0030.028012
X-RAY DIFFRACTIONr_angle_refined_deg1.0911.95411628
X-RAY DIFFRACTIONr_angle_other_deg0.884318371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.27751045
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11723.281381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.571151330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.191556
X-RAY DIFFRACTIONr_chiral_restr0.0630.21296
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219663
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021989
X-RAY DIFFRACTIONr_mcbond_it1.2473.3274195
X-RAY DIFFRACTIONr_mcbond_other1.2463.3274194
X-RAY DIFFRACTIONr_mcangle_it2.0384.9855235
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allWRfactor Rwork
2.35-2.4110.3132660.296562658920.296
2.411-2.4770.3242870.284540356900.284
2.477-2.5480.3062760.272528555610.272
2.548-2.6260.2762660.256515454200.256
2.626-2.7120.2782640.237500152650.237
2.712-2.8070.262750.228478550600.228
2.807-2.9120.2372300.209468049100.209
2.912-3.030.2642540.211448447380.211
3.03-3.1640.2562270.206429645230.206
3.164-3.3170.2292210.194415243730.194
3.317-3.4950.2172100.199392541350.199
3.495-3.7050.2061790.185377339520.185
3.705-3.9590.1962010.177351237130.177
3.959-4.2720.1771890.171326334520.171
4.272-4.6740.1971760.157302832040.157
4.674-5.2160.1991470.166277929260.166
5.216-6.0050.2511100.206248825980.206
6.005-7.3110.2251070.216213522420.216
7.311-10.1590.177910.156167317640.156
10.159-38.6710.264590.222105111100.222
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)
11.4977-0.9991-1.19143.71481.94153.60750.08640.3057-0.148-0.3816-0.23210.2734-0.0252-0.35990.14570.08520.0207-0.00020.0704-0.02290.0517-11.666-6.879-56.484
21.8641-0.7964-0.91163.53930.78012.0768-0.1056-0.0069-0.0662-0.03060.0596-0.01730.1465-0.03090.0460.0379-0.01430.02960.007-0.01180.0272.237-16.601-51.787
35.1999-2.0771-1.52044.35290.75964.65590.20350.4381-1.1254-0.3383-0.15020.74270.9743-0.1185-0.05340.343-0.0804-0.07050.2558-0.19380.5323-27.049-9.06-42.641
42.2249-1.3438-1.08333.05780.37083.2308-0.00290.0583-0.07610.26730.03220.4157-0.2993-0.5945-0.02940.07220.05870.06820.12190.00530.0993-27.34512.749-30.796
51.86240.8557-1.06128.7628-0.35223.34650.02370.36980.2123-0.50390.08910.99050.0305-0.6807-0.11280.24680.04760.02140.1840.04050.1503-27.30414.927-40.132
62.0507-0.4865-1.18270.79980.75743.009-0.149-0.2058-0.12290.18680.12510.12750.2186-0.0010.02390.05170.03170.03820.04960.02930.0494-30.16812.00110.811
74.91723.42321.4369.3560.40063.4570.0043-0.1302-0.6933-0.39460.08950.80860.5977-0.8571-0.09380.2612-0.0212-0.00420.51920.05370.4251-58.9121.33511.045
82.1124-0.9996-0.92731.82410.48732.5123-0.00930.06640.02540.15480.00220.0488-0.0958-0.23020.00710.04060.02960.04710.05250.02250.1066-37.1922.7784.911
91.8741-0.3618-0.96992.27520.36243.148-0.2056-0.0532-0.33230.2680.02980.22680.41220.03220.17590.08310.01020.05440.00960.00280.0824-16.013-4.143-10.508
107.12561.80830.67081.4110.2681.72340.3215-0.8676-0.86160.4282-0.1515-0.01620.58980.2278-0.170.52870.08390.06780.34180.02380.3034-7.798-8.927-6.501
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 335
2X-RAY DIFFRACTION2A336 - 546
3X-RAY DIFFRACTION3A547 - 609
4X-RAY DIFFRACTION4A610 - 730
5X-RAY DIFFRACTION5A731 - 767
6X-RAY DIFFRACTION6B-4 - 350
7X-RAY DIFFRACTION7B351 - 402
8X-RAY DIFFRACTION8B403 - 546
9X-RAY DIFFRACTION9B547 - 741
10X-RAY DIFFRACTION10B742 - 767

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