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- PDB-4mw4: Trypanosoma brucei methionyl-tRNA synthetase in complex with inhi... -

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Basic information

Entry
Database: PDB / ID: 4mw4
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(5-chloro-2-hydroxy-3-iodobenzyl)amino]propyl}-3-thiophen-3-ylurea (Chem 1473)
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-2EB / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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 30, 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)124,99221
Polymers122,8692
Non-polymers2,12319
Water5,368298
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)62,70911
Polymers61,4351
Non-polymers1,27510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.829, 106.063, 207.642
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, 317 molecules

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


Mass: 92.094 Da / Num. of mol.: 9 / 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.: 3 / 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-2EB / 1-{3-[(5-chloro-2-hydroxy-3-iodobenzyl)amino]propyl}-3-thiophen-3-ylurea


Mass: 465.737 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17ClIN3O2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 3.94 Å3/Da / Density % sol: 68.75 %
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 400.00 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: 0.158 / Number: 438944
ReflectionResolution: 2.5→50 Å / Num. obs: 67226 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.158 / Rsym value: 0.158 / Χ2: 1.004 / Net I/σ(I): 4.7
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 6 % / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 1.905 / Rsym value: 0.813 / % possible all: 98.1
Cell measurementReflection used: 438944

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.38 Å
Translation2.5 Å48.38 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: 2.5→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.204 / Occupancy max: 1 / Occupancy min: 0.7 / SU B: 14.865 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.293 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 3395 5.1 %RANDOM
Rwork0.2043 ---
obs0.2057 66951 99.04 %-
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: 157.46 Å2 / Biso mean: 40.291 Å2 / Biso min: 13.31 Å2
Baniso -1Baniso -2Baniso -3
1-4.98 Å2-0 Å2-0 Å2
2---2.13 Å20 Å2
3----2.85 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8442 0 121 298 8861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198765
X-RAY DIFFRACTIONr_bond_other_d0.0020.028328
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.96411892
X-RAY DIFFRACTIONr_angle_other_deg0.717319152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52551052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56723.467398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.518151434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3771558
X-RAY DIFFRACTIONr_chiral_restr0.0660.21315
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219796
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022010
X-RAY DIFFRACTIONr_mcbond_it0.9722.4144224
X-RAY DIFFRACTIONr_mcbond_other0.9722.4144222
X-RAY DIFFRACTIONr_mcangle_it1.7263.6145270
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 (%)
2.5-2.5690.3072400.2964526489097.464
2.569-2.6380.2792300.2584493476699.098
2.638-2.7140.2912090.244425465299.613
2.714-2.7970.2752390.2434245451699.291
2.797-2.8880.2732420.234118439599.204
2.888-2.9880.2622350.2163992424199.67
2.988-3.10.2622220.2063870411199.538
3.1-3.2250.2612010.1993733396699.193
3.225-3.3670.2212120.1833580381999.293
3.367-3.5290.2111760.1873458364499.726
3.529-3.7170.2171410.1873265345398.639
3.717-3.9390.211660.1823137331499.668
3.939-4.2050.1791360.1722949309899.58
4.205-4.5350.1641420.1662752290699.587
4.535-4.9560.1791400.1722537270499.001
4.956-5.5230.2191150.2232298247097.692
5.523-6.3410.2791180.2512043218099.128
6.341-7.6810.2691060.2341774188999.524
7.681-10.5230.18770.1531407151697.889
10.523-300.267450.26591198097.551
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)
10.948-0.7165-0.56441.04360.60930.9451-0.01870.0934-0.0537-0.1773-0.03410.06520.0055-0.09820.05280.1662-0.01810.03730.0481-0.0080.0379-6.542-11.799-56.34
21.2404-0.672-0.4571.73310.33941.693-0.0571-0.0273-0.0427-0.01980.0653-0.00660.054-0.0275-0.00820.1633-0.00850.04550.0566-0.00510.09451.46-14.68-51.011
31.9521-1.3606-1.12116.32390.42953.37050.01560.1808-0.4648-0.1457-0.15070.20090.5381-0.07460.1350.1459-0.0367-0.00170.0723-0.07730.1411-27.812-7.44-42.28
41.3776-0.5403-0.7021.45640.15931.83480.0117-0.0320.00960.08420.03470.1164-0.2633-0.2543-0.04640.10490.04290.03360.07380.00090.0519-26.53513.641-31.593
52.11131.87050.37968.3561-0.5243.6622-0.06910.4155-0.0478-0.50150.35510.8529-0.3298-0.5621-0.28590.17650.08370.01840.20630.03410.1604-31.34513.809-39.694
61.2274-0.1458-0.85990.77020.42211.6091-0.0969-0.1143-0.0660.15060.0160.03610.16540.05780.08090.10070.02170.01070.09660.00130.0273-30.82912.13110.798
72.27762.94591.199110.35290.15345.10670.3857-0.2243-0.2209-0.04510.06980.90861.1711-1.3828-0.45550.436-0.2763-0.24750.42470.10120.3385-61.0619.29810.978
81.0301-0.5511-0.49341.04130.25281.8773-0.01030.06440.01140.0454-0.0235-0.0162-0.0628-0.05460.03390.1098-0.00630.01270.0874-0.00680.0759-37.61322.5394.603
91.6531-0.1577-0.67591.35410.18811.3915-0.0778-0.0289-0.18310.1106-0.02050.08360.250.05620.09830.17690.02250.03530.0595-0.01620.0482-15.409-3.941-10.415
103.24613.4981.81998.87484.43166.3389-0.3229-0.6006-0.9525-0.21160.235-0.78520.43580.35510.08790.46780.12630.06260.27920.24850.3837-15.704-16.944-3.448
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 380
2X-RAY DIFFRACTION2A381 - 546
3X-RAY DIFFRACTION3A547 - 616
4X-RAY DIFFRACTION4A617 - 739
5X-RAY DIFFRACTION5A740 - 767
6X-RAY DIFFRACTION6B-4 - 351
7X-RAY DIFFRACTION7B352 - 404
8X-RAY DIFFRACTION8B405 - 546
9X-RAY DIFFRACTION9B547 - 754
10X-RAY DIFFRACTION10B755 - 767

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