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- PDB-4mw9: Trypanosoma brucei methionyl-tRNA synthetase in complex with inhi... -

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Basic information

Entry
Database: PDB / ID: 4mw9
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3-ethynylbenzyl)amino]propyl}-3-thiophen-3-ylurea (Chem 1478)
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-2EJ / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
B: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,07515
Polymers122,6612
Non-polymers1,41413
Water3,801211
1
A: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9958
Polymers61,3311
Non-polymers6647
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0817
Polymers61,3311
Non-polymers7506
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.026, 105.902, 207.016
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: 61330.715 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, 224 molecules

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


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


Mass: 78.133 Da / Num. of mol.: 5 / 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-2EJ / 1-{3-[(3-ethynylbenzyl)amino]propyl}-3-thiophen-3-ylurea


Mass: 313.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N3OS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 3.93 Å3/Da / Density % sol: 68.73 %
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: BL9-2 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 17, 2011
Diffraction measurementDetails: 0.30 degrees, 4.0 sec, detector distance 350.00 mm
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionAv R equivalents: 0.11 / Number: 225536
ReflectionResolution: 2.65→50 Å / Num. obs: 56721 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Χ2: 1.035 / Net I/σ(I): 7.1
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 4 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 2.045 / Rsym value: 0.692 / % possible all: 100
Cell measurementReflection used: 225536

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.65 Å44.32 Å
Translation2.65 Å44.32 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefmac_5.7.0032refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EG8

4eg8


Resolution: 2.65→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.18 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 16.301 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.337 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 2859 5.1 %RANDOM
Rwork0.1802 ---
obs0.1819 56449 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 149.62 Å2 / Biso mean: 44.8737 Å2 / Biso min: 17.84 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å20 Å20 Å2
2---0.79 Å2-0 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 2.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8492 0 85 211 8788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198793
X-RAY DIFFRACTIONr_bond_other_d0.0010.028356
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.96211938
X-RAY DIFFRACTIONr_angle_other_deg0.72319222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.33951063
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22823.484399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.146151452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.021558
X-RAY DIFFRACTIONr_chiral_restr0.0610.21318
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219875
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022023
X-RAY DIFFRACTIONr_mcbond_it1.0962.8664260
X-RAY DIFFRACTIONr_mcbond_other1.0962.8664261
X-RAY DIFFRACTIONr_mcangle_it1.9034.2935317
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 (%)
2.65-2.720.3391970.283680410494.469
2.72-2.7940.3022120.2623801402399.751
2.794-2.8750.2851860.2353713391399.642
2.875-2.9620.2741810.2223597379299.631
2.962-3.0580.2532140.2093475370099.703
3.058-3.1640.2441750.2133394357999.721
3.164-3.2830.231730.1913269345799.566
3.283-3.4150.2171680.1993141332199.639
3.415-3.5650.211440.1843029318899.529
3.565-3.7360.1981510.1662899306199.641
3.736-3.9350.1921610.1542771294599.559
3.935-4.1690.1721540.1472619278699.533
4.169-4.4510.1861280.1422472260999.655
4.451-4.7980.1581320.1332299244099.631
4.798-5.2430.191950.1542170227899.429
5.243-5.8390.2241220.1831952208199.664
5.839-6.7010.232900.1881746184399.62
6.701-8.1060.193750.1671521160299.625
8.106-11.0670.135630.1311211128199.454
11.067-300.221370.2279683899.403
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)
11.0197-0.7636-0.59961.26510.50620.8909-0.02130.1203-0.1488-0.1452-0.06090.09840.0439-0.13560.08230.1858-0.02510.05990.036-0.01450.0468-5.297-14.992-55.43
21.6771-0.8089-0.54971.79570.65721.9628-0.0327-0.01230.0439-0.06930.0276-0.12140.00280.03960.00510.1606-0.02150.05780.0311-0.0120.08861.908-10.888-50.417
32.1206-0.9931-0.05344.43350.0641.8812-0.05290.2058-0.6442-0.1766-0.04590.42310.4859-0.23720.09880.1468-0.08930.0420.0987-0.09650.216-28.341-8.724-42.243
41.6446-0.6194-0.60391.5860.44761.82520.01180.01420.07050.01160.00130.0999-0.2831-0.3149-0.01310.1330.03780.04130.07210.00170.0408-26.28514.549-32.034
52.63751.6963.09476.4159-5.740315.4690.1648-0.16540.98170.7598-0.0991.7352-0.9345-0.7753-0.06590.3030.22910.13110.8028-0.23140.9628-39.8341.378-43.035
61.6282-0.4041-0.97340.6470.48221.7909-0.1318-0.1713-0.10810.16850.05440.0380.15860.04170.07740.13580.03120.00380.10280.00150.009-30.95112.31410.861
72.94961.85841.25688.3929-0.19623.28940.4041-0.1764-0.4493-0.15270.10260.87630.6755-0.8002-0.50660.2219-0.1203-0.15120.26480.06270.3144-60.61219.50310.759
81.3218-0.8915-0.63951.37310.1661.994-0.02340.03210.05590.0777-0.0013-0.0101-0.0615-0.12320.02470.10350.00290.02030.102-0.01830.0527-37.50122.4744.479
91.75-0.3039-0.80221.23710.27121.65-0.1229-0.0285-0.23050.07680.00020.14250.34370.03810.12270.18660.01860.03190.0694-0.02320.0771-16.981-4.727-10.745
103.0291.27130.35550.83660.40822.07330.2183-0.422-0.46470.3254-0.064-0.18790.490.2453-0.15430.23490.0861-0.04160.12310.05750.0891-6.953-3.532-5.649
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 413
2X-RAY DIFFRACTION2A414 - 546
3X-RAY DIFFRACTION3A547 - 617
4X-RAY DIFFRACTION4A618 - 755
5X-RAY DIFFRACTION5A756 - 768
6X-RAY DIFFRACTION6B-4 - 351
7X-RAY DIFFRACTION7B352 - 405
8X-RAY DIFFRACTION8B406 - 546
9X-RAY DIFFRACTION9B547 - 731
10X-RAY DIFFRACTION10B732 - 767

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