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

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Basic information

Entry
Database: PDB / ID: 4mwc
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-(3-{[(2-methyl-1-benzothiophen-3-yl)methyl]amino}propyl)-3-thiophen-3-ylurea (Chem 1540)
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-2EM / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.649 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 1.2Nov 27, 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)124,47116
Polymers122,8692
Non-polymers1,60214
Water5,801322
1
A: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2239
Polymers61,4351
Non-polymers7888
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2497
Polymers61,4351
Non-polymers8146
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.742, 105.737, 206.294
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, 336 molecules

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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / 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-2EM / 1-(3-{[(2-methyl-1-benzothiophen-3-yl)methyl]amino}propyl)-3-thiophen-3-ylurea


Mass: 359.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21N3OS2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 3.89 Å3/Da / Density % sol: 68.41 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 3, 2011
Diffraction measurementDetails: 0.50 degrees, 30.0 sec, detector distance 62.00 mm
RadiationMonochromator: VariMax HF (Osmic) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionAv R equivalents: 0.121 / Number: 218354
ReflectionResolution: 2.649→50 Å / Num. obs: 56308 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Χ2: 1.062 / Net I/σ(I): 7.5
Reflection shellResolution: 2.649→2.7 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.938 / Rsym value: 0.6 / % possible all: 100
Cell measurementReflection used: 218354

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.65 Å29.54 Å
Translation2.65 Å29.54 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: 2.649→29.55 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.087 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.412 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2552 2858 5.1 %RANDOM
Rwork0.2148 ---
obs0.2168 56253 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.59 Å2 / Biso mean: 36.8537 Å2 / Biso min: 9.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å2-0 Å2-0 Å2
2---1.53 Å2-0 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.649→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8502 0 97 322 8921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198817
X-RAY DIFFRACTIONr_bond_other_d0.0010.028369
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.96311973
X-RAY DIFFRACTIONr_angle_other_deg0.72319255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6951063
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15623.475400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.429151451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2251558
X-RAY DIFFRACTIONr_chiral_restr0.0640.21321
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219902
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022026
X-RAY DIFFRACTIONr_mcbond_it0.8372.1614258
X-RAY DIFFRACTIONr_mcbond_other0.8372.1614259
X-RAY DIFFRACTIONr_mcangle_it1.4853.2375316
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 (%)
2.649-2.7170.332060.2763864409499.414
2.717-2.7910.3242440.26437553999100
2.791-2.8710.3112040.25836683872100
2.871-2.9590.3081950.23535913786100
2.959-3.0550.2831880.23134953683100
3.055-3.1610.2881720.2393380355499.944
3.161-3.2790.2891500.2213283343599.942
3.279-3.4110.2341700.2183156333199.85
3.411-3.5610.2581430.2243016316699.779
3.561-3.7320.271800.2072871305999.738
3.732-3.930.2291440.1992773292799.658
3.93-4.1640.1961410.1822617277199.531
4.164-4.4460.2171230.1782437258698.995
4.446-4.7930.1841090.1772313243799.384
4.793-5.2370.2241180.2042113226398.586
5.237-5.8330.2921070.2431928206598.547
5.833-6.6930.287850.2481723183898.368
6.693-8.0980.26870.2111466159297.55
8.098-11.0560.181610.1481176127597.02
11.056-300.305310.26677083695.813
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)
11.4725-0.4499-0.6961.85960.85951.9060.04380.2274-0.138-0.1118-0.11870.05090.0858-0.22060.07490.16550.02270.01860.0555-0.00380.0415-11.399-6.973-56.725
21.0795-0.4759-0.44921.51640.29691.2712-0.05460.0005-0.0188-0.04540.03590.0330.02940.01180.01870.1428-0.00680.03090.049-0.00830.07652.162-16.43-51.465
31.3549-0.1832-0.36274.66610.61863.3547-0.02870.227-0.6069-0.143-0.04950.2120.6836-0.19190.07820.1616-0.0456-0.00950.0762-0.10650.2808-28.382-8.968-42.307
41.7213-0.4357-0.37051.27210.28291.3521-0.0314-0.0524-0.0030.04010.04530.098-0.2305-0.244-0.01380.11110.04290.03610.06380.00560.0229-26.88813.448-31.32
52.98021.8912-0.53544.6275-0.0113.43580.08060.3645-0.0342-0.2709-0.00450.6880.105-0.5347-0.07610.13310.0451-0.04150.1329-0.02090.1657-30.36512.967-39.41
61.235-0.3557-0.7230.3540.54271.182-0.0737-0.1111-0.07750.0991-0.00680.04340.09680.06720.08050.12510.01270.01520.0905-0.0040.0398-31.17612.10210.825
73.45313.10880.868710.18871.60042.01680.2444-0.1812-0.3932-0.0660.05940.9850.6943-0.6017-0.30380.4147-0.2316-0.20930.34780.16260.4606-60.86819.42410.708
81.0631-0.6425-0.68671.34860.20851.74860.02120.02580.090.0582-0.0236-0.0162-0.0167-0.08890.00240.087-0.00790.01510.078-0.00720.0721-37.79822.454.396
91.7583-0.3221-0.68681.33820.21011.4171-0.076-0.0411-0.16920.04990.00220.12060.24880.03980.07380.14220.02020.02380.0569-0.01670.0484-16.909-4.619-10.364
107.32431.1363-0.01194.7827-0.28372.35180.1297-0.4387-0.61330.47450.0392-0.35450.3670.2431-0.16890.1480.0521-0.06240.0660.01040.0815-7.639-4.818-6.022
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 - 737
5X-RAY DIFFRACTION5A738 - 768
6X-RAY DIFFRACTION6B-4 - 351
7X-RAY DIFFRACTION7B352 - 405
8X-RAY DIFFRACTION8B406 - 545
9X-RAY DIFFRACTION9B546 - 735
10X-RAY DIFFRACTION10B736 - 767

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