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- PDB-4mw1: Trypanosoma brucei methionyl-tRNA synthetase in complex with inhi... -

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Basic information

Entry
Database: PDB / ID: 4mw1
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-thiophen-3-ylurea (Chem 1444)
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-44F / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.494 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
SupersessionApr 30, 2014ID: 3U20
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 1.2Nov 20, 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)124,60618
Polymers122,8692
Non-polymers1,73716
Water7,692427
1
A: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2019
Polymers61,4351
Non-polymers7668
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4059
Polymers61,4351
Non-polymers9718
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.021, 105.754, 206.381
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 , 5 types, 443 molecules

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


Mass: 92.094 Da / Num. of mol.: 10 / 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-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#5: Chemical ChemComp-44F / 1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-thiophen-3-ylurea


Mass: 353.867 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20ClN3O2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 3.91 Å3/Da / Density % sol: 68.53 %
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: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2010
Diffraction measurementDetails: 1.00 degrees, 3.0 sec, detector distance 295.00 mm
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.16 / Number: 497084
ReflectionResolution: 2.494→50 Å / Num. obs: 67803 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.16 / Rsym value: 0.16 / Χ2: 0.953 / Net I/σ(I): 5.4
Reflection shellResolution: 2.494→2.54 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 1.875 / Rsym value: 0.852 / % possible all: 100
Cell measurementReflection used: 497084

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.46 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.27 Å
Translation2.5 Å44.27 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefmac_5.7.0032refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EG8

4eg8


Resolution: 2.494→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.171 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 12.661 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.278 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3427 5.1 %RANDOM
Rwork0.1917 ---
obs0.1932 67503 99.4 %-
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: 132.03 Å2 / Biso mean: 35.617 Å2 / Biso min: 11.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å2-0 Å2-0 Å2
2---1.34 Å2-0 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.494→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8510 0 108 427 9045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198846
X-RAY DIFFRACTIONr_bond_other_d0.0010.028414
X-RAY DIFFRACTIONr_angle_refined_deg1.171.96212003
X-RAY DIFFRACTIONr_angle_other_deg0.726319355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64451068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43323.458402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.917151451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4361559
X-RAY DIFFRACTIONr_chiral_restr0.0630.21325
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219923
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022034
X-RAY DIFFRACTIONr_mcbond_it0.9211.7324273
X-RAY DIFFRACTIONr_mcbond_other0.9211.7334274
X-RAY DIFFRACTIONr_mcangle_it1.6762.5935337
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 (%)
2.494-2.5590.3082380.2784509490796.739
2.559-2.6280.2932480.2514544480099.833
2.628-2.7040.2752390.2294441469299.744
2.704-2.7860.252490.2254254451999.646
2.786-2.8770.242280.2084181442199.729
2.877-2.9770.2472030.2024061427699.719
2.977-3.0880.2432130.2033858409199.511
3.088-3.2130.261930.2033811401999.627
3.213-3.3540.2281950.1933613382099.686
3.354-3.5150.2312050.1933472368299.864
3.515-3.7030.2171540.1773305346799.769
3.703-3.9230.1941690.1663137331599.729
3.923-4.1890.1891380.1612989313499.777
4.189-4.5180.1761700.1532730290899.725
4.518-4.9380.1661280.1572580271999.595
4.938-5.5020.2111210.1932351247899.758
5.502-6.3180.2551110.2112069219199.498
6.318-7.6530.228930.1961798190099.526
7.653-10.4870.147820.1491432151899.736
10.487-300.234490.22492198398.678
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)
10.56760.46860.36950.73140.30420.3978-0.0365-0.01340.02270.04740.0152-0.02130.0101-0.03440.02130.2240.0078-0.05980.1208-0.0110.1598-2.07413.2352.984
20.54130.46670.50170.82190.54380.9549-0.0513-0.04870.1345-0.0346-0.00060.03390.0254-0.1980.05190.1223-0.0091-0.04360.2048-0.00710.1915-27.407-4.72135.467
30.8674-1.1550.40623.9933-0.51131.4220.1713-0.2103-0.04540.02210.05330.29270.246-0.1695-0.22460.1159-0.1164-0.03630.15190.04230.1228-28.856-14.34239.579
40.61570.18270.51850.20430.14290.6088-0.07580.09030.0006-0.04440.0355-0.0259-0.08780.07710.04020.1771-0.0141-0.00760.2071-0.00380.1317-33.295-13.869-10.741
50.0266-0.3460.12767.4435-2.48320.8433-0.01080.0202-0.07380.04220.4771.3798-0.0458-0.1019-0.46630.1999-0.00770.17590.28410.08240.5265-63.359-14.759-10.485
60.45650.44680.39630.60890.08270.9217-0.0049-0.0553-0.0296-0.0524-0.01-0.03210.0182-0.07950.01490.1306-0.0155-0.01990.2185-0.02120.1677-37.998-22.561-4.391
71.01420.23750.77040.48520.24440.6534-0.0842-0.02340.053-0.07070.01580.0753-0.16670.05720.06840.204-0.0508-0.04180.1859-0.01690.1617-16.6693.99610.143
84.0712-0.5782-1.54960.21240.43421.11460.2051-1.08361.1805-0.17240.4913-0.2037-0.32770.8894-0.69640.1767-0.3910.1151.0149-0.36450.6288-7.5528.6526.016
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 545
2X-RAY DIFFRACTION2A546 - 735
3X-RAY DIFFRACTION3A736 - 767
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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