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

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Basic information

Entry
Database: PDB / ID: 4mwd
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-thiophen-3-ylurea (Chem 1433) and ATP analog AMPPCP
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-43E / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.253 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 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)125,34519
Polymers123,0772
Non-polymers2,26817
Water9,314517
1
A: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3099
Polymers61,5391
Non-polymers7708
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,03710
Polymers61,5391
Non-polymers1,4989
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.267, 105.880, 206.676
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: 61538.684 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 , 7 types, 534 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.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / 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-43E / 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-thiophen-3-ylurea


Mass: 358.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17Cl2N3OS
#7: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 3.92 Å3/Da / Density % sol: 68.65 %
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: Dec 12, 2011
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.253→39.967 Å / Num. all: 91992 / Num. obs: 91992 / % possible obs: 99.8 % / Redundancy: 7.8 % / Rsym value: 0.177 / Net I/σ(I): 11.2
Reflection shell

Rmerge(I) obs: 0.012 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.253-2.387.80.6103840133041.24499.9
2.38-2.527.80.998184125740.90199.9
2.52-2.698.11.295303118310.64199.9
2.69-2.917.71.885423110400.42399.9
2.91-3.197.92.580600101950.27799.7
3.19-3.5684.17408392540.16299.9
3.56-4.117.67.56237481620.09199.5
4.11-5.047.910.55563270240.065100
5.04-7.137.610.24135954700.06899.7
7.13-39.9677.213.82272431380.0498.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.25 Å39.97 Å
Translation2.25 Å39.97 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALA3.3.16data scaling
PHASER2.3.0phasing
REFMACrefmac_5.7.0032refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EG8

4eg8


Resolution: 2.253→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.182 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.356 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2114 4606 5 %RANDOM
Rwork0.1816 ---
obs0.1831 91918 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.27 Å2 / Biso mean: 38.6552 Å2 / Biso min: 17.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å2-0 Å2-0 Å2
2---0.06 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.253→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8508 0 138 517 9163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198872
X-RAY DIFFRACTIONr_bond_other_d0.0010.028425
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.96812047
X-RAY DIFFRACTIONr_angle_other_deg0.729319381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50851065
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65223.441401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.898151452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6961559
X-RAY DIFFRACTIONr_chiral_restr0.0680.21330
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219900
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022036
X-RAY DIFFRACTIONr_mcbond_it1.052.5264260
X-RAY DIFFRACTIONr_mcbond_other1.052.5264259
X-RAY DIFFRACTIONr_mcangle_it1.8213.7825319
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 (%)
2.253-2.3110.2933280.2776336668899.641
2.311-2.3740.2983310.2666211654899.908
2.374-2.4430.3213270.2565998634799.653
2.443-2.5170.2962790.2365921620699.903
2.517-2.5990.2733330.2335646598799.866
2.599-2.690.252760.225509579499.845
2.69-2.7910.262820.2045312560699.786
2.791-2.9030.2482600.1955148541799.834
2.903-3.0310.2582490.1984938521699.444
3.031-3.1780.2242300.1894741497999.839
3.178-3.3470.2262370.1884474471699.894
3.347-3.5480.2142340.1794296453899.824
3.548-3.7890.1891950.1614019422899.669
3.789-4.0870.1612160.1453715396899.068
4.087-4.4690.1481920.1313473366699.973
4.469-4.9820.1591810.1331663347100
4.982-5.7270.2071390.1612826297799.597
5.727-6.9510.1991400.1792413256299.649
6.951-9.5770.141000.1361937204799.511
9.577-300.149760.1611205129798.766
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)
10.8439-0.5854-0.41810.84620.39850.72-0.02890.0695-0.0901-0.0215-0.00020.0290.0373-0.0420.02910.1867-0.00750.03340.0396-0.01530.0264-2.82-14.994-53.868
21.3007-0.7546-0.67410.92370.58010.886-0.00860.1667-0.1419-0.0066-0.09240.15660.1082-0.21610.1010.1516-0.030.00670.0587-0.0170.0273-17.091-5.244-45.339
31.2856-0.7186-0.65861.37730.38711.80150.01510.1049-0.046-0.025-0.02860.1605-0.1579-0.32750.01360.13430.01960.02220.08220.00550.0262-26.68412.828-33.063
40.8892-0.4774-0.38780.74070.13821.086-0.0338-0.0019-0.05960.06280.01520.1390.0458-0.16770.01860.1624-0.0150.00530.0901-0.0010.0497-40.63417.3338.505
51.84880.0762-0.20281.4340.52651.67310.0817-0.13090.05570.1428-0.0268-0.140.06230.0933-0.05480.1151-0.01730.00230.0434-0.00040.018-30.94121.1384.631
619.77132.24721.54869.1984-9.11019.7807-0.018-0.6709-0.52710.11680.18080.111-0.0841-0.3674-0.16280.1436-0.11790.14390.1609-0.12930.2224-43.067-5.904-0.372
71.4506-0.4117-0.54940.72610.34741.2765-0.081-0.0193-0.19130.05510.01160.03930.24990.11720.06940.16780.01930.02410.0229-0.0070.0348-14.283-3.907-11.31
87.9621.21170.06723.1796-0.11662.21840.1974-0.6241-0.98360.353-0.1134-0.10810.33940.2029-0.0840.17340.075-0.04090.11390.06280.1257-7.754-7.749-6.449
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 488
2X-RAY DIFFRACTION2A489 - 626
3X-RAY DIFFRACTION3A627 - 768
4X-RAY DIFFRACTION4B-4 - 488
5X-RAY DIFFRACTION5B489 - 546
6X-RAY DIFFRACTION6B547 - 559
7X-RAY DIFFRACTION7B560 - 740
8X-RAY DIFFRACTION8B741 - 767

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