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- PDB-4mw2: Trypanosoma brucei methionyl-tRNA synthetase in complex with inhi... -

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Basic information

Entry
Database: PDB / ID: 4mw2
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-(3-{[5-chloro-2-hydroxy-3-(prop-2-en-1-yl)benzyl]amino}propyl)-3-thiophen-3-ylurea (Chem 1472)
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-2E9 / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 9, 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)125,27925
Polymers122,8692
Non-polymers2,40923
Water4,846269
1
A: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,82116
Polymers61,4351
Non-polymers1,38715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4579
Polymers61,4351
Non-polymers1,0238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.712, 106.080, 206.275
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, 292 molecules

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


Mass: 92.094 Da / Num. of mol.: 12 / 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.: 4 / 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-2E9 / 1-(3-{[5-chloro-2-hydroxy-3-(prop-2-en-1-yl)benzyl]amino}propyl)-3-thiophen-3-ylurea


Mass: 379.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22ClN3O2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 68.5 %
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: Jun 19, 2011
Diffraction measurementDetails: 1.00 degrees, 10.0 sec, detector distance 430.02 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: 0.106 / Number: 528641
ReflectionResolution: 2.3→50 Å / Num. obs: 82816 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Χ2: 1.017 / Net I/σ(I): 5.8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 2 / Rsym value: 0.728 / % possible all: 88.7
Cell measurementReflection used: 528641

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.2 Å
Translation2.5 Å48.2 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: 2.3→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.503 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 4125 5 %RANDOM
Rwork0.2026 ---
obs0.2043 82518 95.94 %-
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: 154.44 Å2 / Biso mean: 47.5478 Å2 / Biso min: 23.64 Å2
Baniso -1Baniso -2Baniso -3
1-7.4 Å2-0 Å2-0 Å2
2---4.31 Å2-0 Å2
3----3.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8416 0 146 269 8831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198778
X-RAY DIFFRACTIONr_bond_other_d0.0010.028330
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.96511910
X-RAY DIFFRACTIONr_angle_other_deg0.734319157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.44551054
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40823.476397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.902151427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8641557
X-RAY DIFFRACTIONr_chiral_restr0.0650.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219806
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022013
X-RAY DIFFRACTIONr_mcbond_it0.9162.374222
X-RAY DIFFRACTIONr_mcbond_other0.9162.374223
X-RAY DIFFRACTIONr_mcangle_it1.5523.555271
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 (%)
2.3-2.3610.3092670.2975180626586.943
2.361-2.4260.3162570.2935228606790.407
2.426-2.4960.3043300.2735053593390.73
2.496-2.5720.2772630.2615215575195.253
2.572-2.6560.2972910.2515118560796.469
2.656-2.7480.2682510.245038540597.854
2.748-2.8510.262630.2364904524198.588
2.851-2.9660.2762470.2264687503398.033
2.966-3.0970.2832250.2164392485195.176
3.097-3.2460.2572180.2094389465498.99
3.246-3.4190.2382080.1984184443099.142
3.419-3.6240.2412140.1923952419099.427
3.624-3.870.2181850.1793758396499.47
3.87-4.1740.1811830.163371371695.64
4.174-4.5640.1981490.1513244339899.853
4.564-5.0880.1841810.1672935313099.553
5.088-5.8470.2411170.1982552278395.904
5.847-7.0940.2761340.2122227238898.869
7.094-9.7630.166750.161831192299.168
9.763-300.204650.1951090120895.613
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)
11.2045-0.3738-0.81912.35740.63172.22040.00560.2386-0.0576-0.2403-0.10960.17130.1348-0.30420.1040.06020.01660.01120.25440.01250.159-11.495-7.332-56.687
21.3407-0.7485-0.61712.50790.63381.7944-0.058-0.0070.0094-0.04970.05120.02790.0591-0.00730.00680.0145-0.0030.03310.1905-0.00480.16112.202-16.641-51.411
31.8579-0.5814-0.53974.35170.14123.5368-0.08840.1815-0.512-0.21690.04030.2630.5634-0.08560.04810.1109-0.05570.03550.3982-0.06790.3958-27.895-7.748-41.916
41.2698-0.6324-0.55421.53380.11642.0357-0.0208-0.02970.00350.05140.04460.1851-0.2396-0.3038-0.02380.03770.0380.02580.27260.02020.1985-26.51413.411-31.501
51.67881.60861.118612.2894-0.07274.0393-0.14510.59210.1646-0.67360.31211.68490.0333-0.4049-0.1670.26170.03560.04330.55360.04010.3741-32.8611.525-39.82
61.3576-0.2972-0.76471.0210.41311.7874-0.0667-0.1572-0.05260.20530.00180.05320.11470.06820.06490.04950.01880.00850.2609-0.00440.1481-30.86612.21710.924
73.81770.14090.22847.1577-0.26922.47710.1315-0.0177-0.82540.02170.15121.4021.0007-0.8535-0.28270.5619-0.1429-0.05830.67340.0770.5932-61.18819.41811.038
81.4701-0.69-0.76221.72350.25032.4950.04160.09110.09970.0805-0.0035-0.039-0.0196-0.1103-0.03810.01880.01090.04510.225-0.01070.18-37.71922.5924.594
91.1832-0.1931-0.62531.68020.22122.1483-0.0755-0.0127-0.23480.1398-0.03530.11540.31780.05340.11070.08420.02310.01680.2434-0.00740.1926-16.735-4.578-10.294
104.54481.28221.23781.16130.48342.55130.2731-0.1811-0.62970.5294-0.0611-0.26690.51350.3642-0.21210.34860.0896-0.04330.4387-0.04410.3365-7.491-4.789-6.128
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 337
2X-RAY DIFFRACTION2A338 - 546
3X-RAY DIFFRACTION3A547 - 616
4X-RAY DIFFRACTION4A617 - 740
5X-RAY DIFFRACTION5A741 - 768
6X-RAY DIFFRACTION6B-4 - 351
7X-RAY DIFFRACTION7B352 - 403
8X-RAY DIFFRACTION8B404 - 546
9X-RAY DIFFRACTION9B547 - 735
10X-RAY DIFFRACTION10B736 - 767

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