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

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Basic information

Entry
Database: PDB / ID: 4mwe
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-(3-{[5-chloro-3-(prop-2-en-1-yl)-2-(prop-2-en-1-yloxy)benzyl]amino}propyl)-3-thiophen-3-ylurea (Chem 1475)
ComponentsMethionyl-tRNA synthetase
KeywordsLIGASE/LIGASE INHIBITOR / aminoacyl-tRNA synthetase / aaRS / MetRS / parasite / protein-inhibitor complex / Rossmann fold / translation / nucleotide binding / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ciliary plasm / mitochondrion / 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-2EN / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT OF ISOMORPHOUS STRUCTURE / Resolution: 2.45 Å
AuthorsKoh, C.Y. / Kim, J.E. / Wetzel, A.B. / de van der Schueren, W.J. / Shibata, S. / Liu, J. / Zhang, Z. / Fan, E. / Verlinde, C.L.M.J. / Hol, W.G.J.
CitationJournal: Plos Negl Trop Dis / Year: 2014
Title: Structures of Trypanosoma brucei Methionyl-tRNA Synthetase with Urea-Based Inhibitors Provide Guidance for Drug Design against Sleeping Sickness.
Authors: Koh, C.Y. / Kim, J.E. / Wetzel, A.B. / de van der Schueren, W.J. / Shibata, S. / Ranade, R.M. / Liu, J. / Zhang, Z. / Gillespie, J.R. / Buckner, F.S. / Verlinde, C.L. / Fan, E. / Hol, W.G.
History
DepositionSep 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)124,68018
Polymers122,8692
Non-polymers1,81116
Water4,648258
1
A: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,28310
Polymers61,4351
Non-polymers8489
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3978
Polymers61,4351
Non-polymers9637
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.448, 106.086, 206.505
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 (eukaryote) / 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, 274 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#6: Chemical ChemComp-2EN / 1-(3-{[5-chloro-3-(prop-2-en-1-yl)-2-(prop-2-en-1-yloxy)benzyl]amino}propyl)-3-thiophen-3-ylurea


Mass: 419.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26ClN3O2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 68.44 %
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 6.0-6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
PH range: 6.0-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2011
Diffraction measurementDetails: 1.00 degrees, 10.0 sec, detector distance 420.00 mm
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionAv R equivalents: 0.146 / Number: 381757
ReflectionResolution: 2.45→50 Å / Num. obs: 70116 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.141 / Rsym value: 0.141 / Χ2: 1.063 / Net I/σ(I): 6.6
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0 / Mean I/σ(I) obs: 1.97 / Rsym value: 0 / % possible all: 99.8
Cell measurementReflection used: 381757

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.7.0032refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: RIGID BODY REFINEMENT OF ISOMORPHOUS STRUCTURE
Starting model: PDB ENTRY 4EG8

4eg8


Resolution: 2.45→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.204 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.684 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.273 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 3531 5.1 %RANDOM
Rwork0.2036 ---
obs0.205 69868 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 160.74 Å2 / Biso mean: 49.0462 Å2 / Biso min: 20.23 Å2
Baniso -1Baniso -2Baniso -3
1-6.64 Å20 Å2-0 Å2
2---3.79 Å2-0 Å2
3----2.85 Å2
Refinement stepCycle: LAST / Resolution: 2.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8436 0 111 258 8805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198779
X-RAY DIFFRACTIONr_bond_other_d0.0010.028351
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.96211914
X-RAY DIFFRACTIONr_angle_other_deg0.712319211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.17251057
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55223.434399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.444151442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2861558
X-RAY DIFFRACTIONr_chiral_restr0.0620.21315
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219831
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022027
X-RAY DIFFRACTIONr_mcbond_it1.4083.34225
X-RAY DIFFRACTIONr_mcbond_other1.4083.3014226
X-RAY DIFFRACTIONr_mcangle_it2.4144.945274
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 (%)
2.45-2.5170.282570.2714725516096.55
2.517-2.5860.2722560.2534730501899.362
2.586-2.660.282520.2384609488599.509
2.66-2.7410.2972350.2324503476099.538
2.741-2.830.282330.2174337461499.046
2.83-2.9290.2542200.2164174446398.454
2.929-3.0380.2232150.1994074432499.191
3.038-3.1610.2192060.2023922415299.422
3.161-3.30.2661940.1973778401398.978
3.3-3.4590.241870.1913581382798.458
3.459-3.6430.2221990.1863417366598.663
3.643-3.8610.1961570.1813212345697.483
3.861-4.1220.2261600.1763071328298.446
4.122-4.4460.1811400.1662859305898.071
4.446-4.8590.2071420.1782635284397.679
4.859-5.4150.2291220.2192364256796.845
5.415-6.2190.2741150.2572128231896.764
6.219-7.5370.245980.2311823197097.513
7.537-10.3370.187890.1681437158996.035
10.337-300.204530.263915102894.163
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)
10.9050.7060.46561.14990.35190.8572-0.0088-0.03230.01290.06710.00560.0031-0.0279-0.05220.00320.07630.0128-0.05010.1018-0.00790.092-2.18313.47853.061
20.98680.59260.50231.53760.35471.5436-0.0374-0.02950.16790.02530.01340.1105-0.0266-0.21150.0240.0139-0.0026-0.03650.17510.01710.1235-27.22-5.6335.159
32.2672-1.0550.67027.93750.05552.28650.2999-0.382-0.17760.1425-0.01470.79550.1079-0.1444-0.28520.103-0.0896-0.00680.08830.02060.1175-29.812-13.13539.785
40.80.27610.68080.48180.30711.1539-0.0890.10450.0398-0.10930.01040.0186-0.11520.08310.07860.0594-0.0089-0.02880.1571-0.0070.0718-33.151-13.726-11.096
53.3753.97270.56248.4539-1.95481.9836-0.16370.11621.03630.17460.3091.5662-0.5801-0.2577-0.14540.9320.62990.37060.45150.32890.5284-62.441-16.841-10.525
60.64880.38670.53240.9940.40671.10670.0319-0.0989-0.0303-0.0317-0.0217-0.0170.0489-0.0939-0.01010.0311-0.0333-0.0440.16780.00080.0959-37.64-22.616-4.589
71.1790.2140.76960.8230.27591.1758-0.13760.0090.0735-0.11780.04680.1008-0.2380.06020.09080.0989-0.0249-0.03260.1183-0.01050.0742-16.5174.16110.237
812.2462-3.0454-0.80582.20941.15742.41570.02570.03531.4941-0.65540.3765-0.5246-0.64170.6729-0.40220.3158-0.22440.09640.2053-0.08520.2217-7.5068.9515.957
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A237 - 545
2X-RAY DIFFRACTION2A546 - 735
3X-RAY DIFFRACTION3A736 - 768
4X-RAY DIFFRACTION4B-4 - 362
5X-RAY DIFFRACTION5B363 - 403
6X-RAY DIFFRACTION6B404 - 546
7X-RAY DIFFRACTION7B547 - 741
8X-RAY DIFFRACTION8B742 - 767

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