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

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Basic information

Entry
Database: PDB / ID: 4ega
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor Chem 1320
ComponentsMethionyl-tRNA synthetase, putativeMethionine—tRNA ligase
KeywordsLIGASE/LIGASE INHIBITOR / aminoacyl-tRNA synthetase / aaRS / MetRS / parasite / ligase / protein-inhibitor complex / Rossmann-fold / translation / nucleotide binding / Rossmann Fold / tRNA binding / ATP binding / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ciliary plasm / 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-0P8 / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.698 Å
AuthorsKoh, C.Y. / Kim, J.E. / Shibata, S. / Fan, E. / Verlinde, C.L.M.J. / Hol, W.G.J.
CitationJournal: Structure / Year: 2012
Title: Distinct States of Methionyl-tRNA Synthetase Indicate Inhibitor Binding by Conformational Selection.
Authors: Koh, C.Y. / Kim, J.E. / Shibata, S. / Ranade, R.M. / Yu, M. / Liu, J. / Gillespie, J.R. / Buckner, F.S. / Verlinde, C.L. / Fan, E. / Hol, W.G.
History
DepositionMar 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionyl-tRNA synthetase, putative
B: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,93029
Polymers123,0772
Non-polymers2,85327
Water5,441302
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A: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,82915
Polymers61,5391
Non-polymers1,29114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,10114
Polymers61,5391
Non-polymers1,56213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.536, 105.921, 207.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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, putative / Methionine—tRNA ligase


Mass: 61538.684 Da / Num. of mol.: 2 / Fragment: RESIDUES 235-773 / Mutation: K452A, K453R, E454A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / 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, 329 molecules

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


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-MET / METHIONINE / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-0P8 / 2-({3-[(3,5-dibromo-2-methoxybenzyl)amino]propyl}amino)quinolin-4(1H)-one


Mass: 495.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21Br2N3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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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: 3.86 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2.0 to 2.3M ammonium sulfate, 0.2M sodium chloride and 0.1M sodium cacodylate pH 6.0 to 6.6, vapor diffusion, sitting drop, temperature 298K
PH range: 6.0 to 6.6

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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: Apr 2, 2011
RadiationMonochromator: VariMax HF (Osmic) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.698→50 Å / Num. obs: 52915 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.698-2.756.10.822199.6
2.75-2.86.10.769199.3
2.8-2.856.10.662199.8
2.85-2.9160.622199.3
2.91-2.9760.54199.4
2.97-3.0460.431199.1
3.04-3.1260.412198.7
3.12-3.260.345198.8
3.2-3.360.289198.8
3.3-3.460.246198.7
3.4-3.525.90.197198.5
3.52-3.665.90.153198.5
3.66-3.835.90.124198.6
3.83-4.035.90.108199.1
4.03-4.295.90.086199.3
4.29-4.6260.076199.4
4.62-5.086.30.0721100
5.08-5.816.80.0891100
5.81-7.327.10.0871100
7.32-506.80.048198.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.31 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å31.45 Å
Translation2.7 Å31.45 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefmac_5.6.0117refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U1Z

3u1z
PDB Unreleased entry


Resolution: 2.698→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 19.631 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.409 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22762 2664 5.1 %RANDOM
Rwork0.18756 ---
obs0.18959 49997 98.74 %-
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 mean: 46.776 Å2
Baniso -1Baniso -2Baniso -3
1-5.83 Å20 Å20 Å2
2---2.46 Å20 Å2
3----3.36 Å2
Refinement stepCycle: LAST / Resolution: 2.698→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8428 0 171 302 8901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.028833
X-RAY DIFFRACTIONr_bond_other_d0.0010.026055
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.97111970
X-RAY DIFFRACTIONr_angle_other_deg0.8443.00114672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50851057
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9423.424403
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.412151445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6041560
X-RAY DIFFRACTIONr_chiral_restr0.0640.21326
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219639
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021852
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.698→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 189 -
Rwork0.258 3378 -
obs--98.59 %
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)
10.9902-0.5412-0.40091.20070.26140.8382-0.03160.0394-0.0572-0.06760.01280.0264-0.0133-0.05760.01880.0859-0.01220.03950.1814-0.01090.1909-2.264-13.472-53.447
21.1271-0.7745-0.61.80170.48811.6208-0.05470.026-0.14820.0595-0.01080.15120.0475-0.18380.06550.0077-0.00680.03680.2389-0.00330.2111-26.8445.675-35.297
30.0998-0.0095-0.15149.3505-0.80063.80130.06850.10680.1584-0.25090.18831.05080.007-0.2789-0.25680.05940.08530.06860.21820.12350.4201-30.78412.474-39.802
40.9425-0.1707-0.45940.44140.19240.8883-0.0607-0.0966-0.02050.120.0551-0.03180.12630.05640.00560.09180.01380.03290.23290.01380.1843-32.66813.50710.998
51.76820.0008-0.44637.15411.27460.34540.6590.04150.06291.4935-0.67990.44720.1301-0.10490.02090.8348-0.0916-0.05130.4331-0.05730.4364-63.24116.82210.832
61.0694-0.7658-0.68520.70990.23312.01450.00780.07950.08970.0663-0.02020.00060.0362-0.14890.01240.05650.03710.03750.2066-0.00230.1947-37.40522.6334.678
71.5419-0.0517-0.88791.39490.19661.5882-0.12980.0559-0.17940.1237-0.00390.1620.2381-0.02830.13360.07140.01510.05470.1932-0.01830.2038-17.027-4.934-10.915
83.850.7904-0.1980.32610.05651.5173-0.0655-0.3061-0.34890.10930.0658-0.11370.21430.2818-0.00030.11040.10960.00140.29460.02120.2646-6.781-3.997-5.715
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 545
2X-RAY DIFFRACTION2A546 - 737
3X-RAY DIFFRACTION3A738 - 768
4X-RAY DIFFRACTION4B-4 - 362
5X-RAY DIFFRACTION5B363 - 402
6X-RAY DIFFRACTION6B403 - 545
7X-RAY DIFFRACTION7B546 - 731
8X-RAY DIFFRACTION8B732 - 767

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