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- PDB-4eg4: Trypanosoma brucei methionyl-tRNA synthetase in complex with inhi... -

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Basic information

Entry
Database: PDB / ID: 4eg4
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor Chem 1289
ComponentsMethionyl-tRNA synthetase, putative
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 / 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-0OT / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.151 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
Revision 1.4Oct 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, putative
B: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,14331
Polymers123,0772
Non-polymers3,06529
Water3,045169
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A: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,10618
Polymers61,5391
Non-polymers1,56717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,03713
Polymers61,5391
Non-polymers1,49812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.478, 105.892, 207.553
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


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, 198 molecules

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


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / 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-0OT / 2-({3-[(3,5-dibromo-2-ethoxybenzyl)amino]propyl}amino)quinolin-4(1H)-one


Mass: 509.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23Br2N3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 3.91 Å3/Da / Density % sol: 68.5 %
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 1, 2011
RadiationMonochromator: VariMax HF (Osmic) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 35645 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.188 / Net I/σ(I): 5.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.1-3.154.30.7241100
3.15-3.214.30.641100
3.21-3.274.30.5811100
3.27-3.344.30.5121100
3.34-3.414.30.4751100
3.41-3.494.30.414199.9
3.49-3.584.40.3361100
3.58-3.684.40.283199.8
3.68-3.784.40.2441100
3.78-3.914.40.232199.8
3.91-4.044.50.195199.9
4.04-4.214.50.171100
4.21-4.44.50.157199.9
4.4-4.634.50.143199.8
4.63-4.924.60.132199.9
4.92-5.34.60.139199.8
5.3-5.834.70.155199.9
5.83-6.674.70.149199.6
6.67-8.44.70.094199.5
8.4-504.50.056196.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.48 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.15 Å37.9 Å
Translation3.15 Å37.9 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 3U1E

3u1e
PDB Unreleased entry


Resolution: 3.151→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 34.046 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23977 1714 5.1 %RANDOM
Rwork0.19144 ---
obs0.19395 32066 99.03 %-
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: 38.152 Å2
Baniso -1Baniso -2Baniso -3
1-3.76 Å20 Å20 Å2
2---1.81 Å20 Å2
3----1.95 Å2
Refinement stepCycle: LAST / Resolution: 3.151→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8250 0 186 169 8605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.028632
X-RAY DIFFRACTIONr_bond_other_d0.0010.025883
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.97211696
X-RAY DIFFRACTIONr_angle_other_deg0.8383.00114248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73851028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40823.445389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34151382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4521556
X-RAY DIFFRACTIONr_chiral_restr0.0630.21302
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219399
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021804
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: 3.151→3.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 101 -
Rwork0.276 2129 -
obs--98.07 %
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)
11.34490.8386-0.42871.4754-0.2081.2516-0.0409-0.0569-0.06160.16230.0152-0.02880.02780.07830.02570.16240.00810.04720.0785-0.00510.08712.239-13.30553.747
21.95691.236-0.96931.9551-0.57641.8136-0.0037-0.0613-0.1705-0.0495-0.0187-0.2470.04810.210.02240.11580.00690.03070.1128-0.01760.089626.1126.04635.28
30.3831-0.2588-0.8377.70814.51364.20240.0585-0.2194-0.08070.52030.5734-1.1482-0.01830.4306-0.63190.25070.05170.04170.47180.07840.332330.95612.77539.822
41.35530.8787-0.81180.815-0.30061.915-0.03080.105-0.0699-0.04410.0586-0.09010.17230.0308-0.02780.1880.00040.02270.1122-0.00560.07932.44813.486-10.864
50.0173-0.0104-0.00540.01170.00480.00440.09240.0870.04490.0146-0.0621-0.0626-0.0008-0.0122-0.03030.96730.117-0.24560.81710.16120.606961.09418.305-9.809
61.69550.7992-0.74511.4884-0.35992.79430.0075-0.01260.0717-0.1328-0.034-0.0391-0.02410.22240.02650.1517-0.02510.02630.0764-0.02370.103838.77123.058-5.339
71.76770.3797-0.92512.2254-0.65572.2329-0.19120.0099-0.268-0.11780.0235-0.2460.30760.12250.16770.19140.00520.03510.0851-0.00910.074917.164-4.21110.973
85.2956-1.02491.60690.5164-1.18392.89170.15880.7073-0.8834-0.2009-0.01720.12760.4936-0.1072-0.14170.1591-0.0637-0.00560.2168-0.09280.26586.915-3.4895.839
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 538
2X-RAY DIFFRACTION2A539 - 737
3X-RAY DIFFRACTION3A738 - 768
4X-RAY DIFFRACTION4B-4 - 360
5X-RAY DIFFRACTION5B361 - 376
6X-RAY DIFFRACTION6B398 - 540
7X-RAY DIFFRACTION7B541 - 731
8X-RAY DIFFRACTION8B732 - 767

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