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

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Basic information

Entry
Database: PDB / ID: 4mvw
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-thiophen-3-ylurea (Chem 1433)
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 / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.901 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: 3U1Z
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)124,71617
Polymers123,0772
Non-polymers1,63915
Water4,828268
1
A: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2919
Polymers61,5391
Non-polymers7528
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4268
Polymers61,5391
Non-polymers8877
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.066, 105.858, 206.974
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 , 6 types, 283 molecules

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


Mass: 92.094 Da / Num. of mol.: 7 / 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-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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 68.62 %
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 23, 2010
Diffraction measurementDetails: 0.50 degrees, 90.0 sec, detector distance 70.00 mm
RadiationMonochromator: VariMax HF (Osmic) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionAv R equivalents: 0.202 / Number: 290946
ReflectionResolution: 2.901→50 Å / Num. obs: 43617 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.202 / Rsym value: 0.202 / Χ2: 1.067 / Net I/σ(I): 4.7
Reflection shellResolution: 2.901→3 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 2.058 / Rsym value: 0.831 / % possible all: 100
Cell measurementReflection used: 290946

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 33.66 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.9 Å41.55 Å
Translation2.9 Å41.55 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefmac_5.7.0032refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EG8

4eg8


Resolution: 2.901→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.881 / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.193 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 25.502 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.713 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 2185 5 %RANDOM
Rwork0.1927 ---
obs0.1955 43364 99.28 %-
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: 167.51 Å2 / Biso mean: 43.0186 Å2 / Biso min: 7.66 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å2-0 Å2-0 Å2
2---0.89 Å2-0 Å2
3----1.84 Å2
Refinement stepCycle: LAST / Resolution: 2.901→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8487 0 98 268 8853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0198818
X-RAY DIFFRACTIONr_bond_other_d0.0010.028398
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.96311965
X-RAY DIFFRACTIONr_angle_other_deg0.702319322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.28951060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53623.483402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.478151454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5161558
X-RAY DIFFRACTIONr_chiral_restr0.0580.21318
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022025
X-RAY DIFFRACTIONr_mcbond_it0.7362.4844246
X-RAY DIFFRACTIONr_mcbond_other0.7362.4844245
X-RAY DIFFRACTIONr_mcangle_it1.3253.7245304
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 (%)
2.901-2.9760.3191650.2832923315297.97
2.976-3.0560.3241670.2742919309499.741
3.056-3.1440.2871440.2612839300199.4
3.144-3.240.3121590.2282714287999.792
3.24-3.3450.2691450.2182668282599.575
3.345-3.460.2791260.2062600274099.489
3.46-3.5890.2451330.1982497264199.583
3.589-3.7340.2471350.1882407254999.725
3.734-3.8970.2061230.1722328246199.594
3.897-4.0840.2041090.1652237236099.407
4.084-4.30.231200.1532112224299.554
4.3-4.5550.204860.1532015210899.668
4.555-4.8620.22860.161938203199.655
4.862-5.240.247890.1741775187399.519
5.24-5.7220.261850.1831654175099.371
5.722-6.3690.298690.2141512159299.309
6.369-7.2990.279870.2091340143799.304
7.299-8.8110.19660.1711152122799.267
8.811-11.9550.161480.13193198998.989
11.955-300.255430.25561666898.653
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)
11.5556-1.5286-0.62912.82040.64891.4479-0.04840.0749-0.0812-0.09690.00560.10370.054-0.18040.04290.0647-0.01820.03240.051-0.00150.0278-2.705-13.4103-52.938
22.7655-0.7023-0.51351.73130.46382.59090.01530.1302-0.215-0.0748-0.04520.3088-0.0636-0.33750.02990.0368-0.00540.00040.09580.00110.0665-27.40488.9243-34.7723
32.72821.4329-1.019811.3624-12.849915.15491.0418-0.27490.43580.58510.19552.0103-0.5717-0.3158-1.23730.3861-0.0011-0.06760.5626-0.21892.1379-39.39212.3078-42.1648
42.2058-0.8832-1.1481.09380.29461.8574-0.1287-0.1373-0.11320.12470.07250.10950.1178-0.01550.05620.0704-0.0022-0.0010.04140.00350.0172-32.754613.817110.8542
50.5657-0.3875-1.201912.0718-1.11673.9582-0.26880.1521-0.4316-0.25150.37741.45661.2344-0.6675-0.10860.5305-0.1031-0.25860.71830.17041.1032-63.363514.697911.0755
62.5757-0.5874-1.07741.6670.59812.9004-0.0790.09910.0240.07370.0209-0.04810.0843-0.10030.05810.009-0.00120.00930.0083-0.00040.0333-37.664421.87894.2803
72.1733-0.399-0.85042.22550.38792.3597-0.0605-0.1449-0.36890.0783-0.01720.10430.30640.04230.07770.09310.03730.00280.06060.00980.0749-14.7158-4.1098-10.2503
82.5984-0.48344.80951.13321.391313.93290.5985-1.2193-1.1362-0.00560.73680.511.3664-1.1439-1.33530.7957-0.0629-0.2230.88470.5811.243-16.6384-17.1867-3.8721
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A237 - 562
2X-RAY DIFFRACTION2A563 - 756
3X-RAY DIFFRACTION3A757 - 767
4X-RAY DIFFRACTION4B-4 - 362
5X-RAY DIFFRACTION5B363 - 403
6X-RAY DIFFRACTION6B404 - 549
7X-RAY DIFFRACTION7B550 - 756
8X-RAY DIFFRACTION8B757 - 767

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