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- PDB-4mw5: Trypanosoma brucei methionyl-tRNA synthetase in complex with inhi... -

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Basic information

Entry
Database: PDB / ID: 4mw5
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-phenylurea (Chem 1415)
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-415 / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.347 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: 3U1G
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)124,51217
Polymers122,8692
Non-polymers1,64215
Water9,800544
1
A: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0167
Polymers61,4351
Non-polymers5826
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,49510
Polymers61,4351
Non-polymers1,0619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.449, 105.728, 206.592
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, 559 molecules

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


Mass: 92.094 Da / Num. of mol.: 8 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-415 / 1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-phenylurea


Mass: 347.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22ClN3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 68.35 %
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: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2010
Diffraction measurementDetails: 1.00 degrees, 5.0 sec, detector distance 295.01 mm
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.132 / Number: 595828
ReflectionResolution: 2.347→50 Å / Num. obs: 80839 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Χ2: 1.013 / Net I/σ(I): 6.9
Reflection shellResolution: 2.347→2.39 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 2.077 / Rsym value: 0.876 / % possible all: 99.9
Cell measurementReflection used: 595828

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.25 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.16 Å
Translation2.5 Å48.16 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: 2.347→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.217 / WRfactor Rwork: 0.189 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 9.497 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 4039 5 %RANDOM
Rwork0.1886 ---
obs0.1901 80530 99.58 %-
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: 136.8 Å2 / Biso mean: 36.8481 Å2 / Biso min: 15.43 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å2-0 Å20 Å2
2---1.55 Å2-0 Å2
3----1.9 Å2
Refinement stepCycle: LAST / Resolution: 2.347→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8450 0 102 544 9096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198811
X-RAY DIFFRACTIONr_bond_other_d0.0010.028389
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9611958
X-RAY DIFFRACTIONr_angle_other_deg0.728319291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62951063
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44923.367401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.743151451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7721560
X-RAY DIFFRACTIONr_chiral_restr0.0680.21318
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219894
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022038
X-RAY DIFFRACTIONr_mcbond_it0.9982.1334250
X-RAY DIFFRACTIONr_mcbond_other0.9982.1334251
X-RAY DIFFRACTIONr_mcangle_it1.7533.195310
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 (%)
2.347-2.4080.2773040.2455522589798.796
2.408-2.4730.272700.2345397567999.789
2.473-2.5440.2462700.2115299558099.803
2.544-2.6220.2062710.1995112539399.815
2.622-2.7070.2282940.1874967527299.791
2.707-2.8020.2292390.184860511799.648
2.802-2.9060.2012440.1774630489099.673
2.906-3.0240.232630.1724482475899.727
3.024-3.1570.2262210.1824306454199.692
3.157-3.3090.2092150.1814128435699.702
3.309-3.4860.2112120.1823932416099.615
3.486-3.6940.2061980.1783755396399.748
3.694-3.9450.1722050.1693506371699.865
3.945-4.2550.2011650.1633294347299.626
4.255-4.6510.1861520.1593058321999.72
4.651-5.1850.1851320.1792797293999.66
5.185-5.9570.2711500.2322449261299.502
5.957-7.2260.2631090.2532141225799.69
7.226-9.9340.207690.1771726180099.722
9.934-300.259540.2371085114999.13
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)
11.17320.85240.5831.280.44520.998-0.0281-0.040.0340.08510.0138-0.0023-0.0292-0.02430.01430.08040.0163-0.05410.0363-0.01970.0903-2.113.36953.069
21.59560.76920.58481.53390.50891.9789-0.0392-0.08990.2503-0.0091-0.02860.1486-0.0394-0.28360.06790.0090.0048-0.03140.11610.00010.1301-27.349-5.24735.149
33.0927-0.93741.2699.72370.41922.46320.1283-0.3626-0.31380.31710.02340.8120.1089-0.4527-0.15160.1419-0.083-0.01060.13990.05990.0957-29.429-13.35239.692
41.14910.26470.59090.32820.32691.1252-0.10780.15420.0603-0.08640.032-0.0109-0.16350.08830.07580.0573-0.0108-0.02090.13160.00030.0889-30.913-12.364-10.609
54.48842.0038-0.10688.2759-0.3644.01790.10110.15560.78360.21240.39021.7178-0.5457-0.9341-0.49130.08090.11760.10720.31570.16420.4364-60.573-19.817-10.656
61.02510.5520.76381.18710.28941.880.0288-0.0506-0.0768-0.058-0.0126-0.01430.0452-0.0906-0.01620.00960.0009-0.0190.1048-0.01680.0965-37.838-22.554-4.342
71.49260.39360.82731.05780.52581.47-0.12380.01710.1769-0.10620.01050.1011-0.30990.0710.11330.0768-0.0243-0.03030.0715-0.00480.0989-16.7044.07810.141
813.6054-2.12090.233.4078-0.48082.3669-0.0270.46341.7438-0.13930.0141-0.866-0.53880.3290.01290.2367-0.07110.04690.1988-0.01060.354-7.4128.636.194
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A239 - 545
2X-RAY DIFFRACTION2A546 - 735
3X-RAY DIFFRACTION3A736 - 768
4X-RAY DIFFRACTION4B-4 - 352
5X-RAY DIFFRACTION5B353 - 403
6X-RAY DIFFRACTION6B404 - 546
7X-RAY DIFFRACTION7B547 - 741
8X-RAY DIFFRACTION8B742 - 767

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