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- PDB-4eg6: Trypanosoma brucei methionyl-tRNA synthetase in complex with inhi... -

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Basic information

Entry
Database: PDB / ID: 4eg6
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor Chem 1325
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-0P5 / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.901 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 1.4Nov 6, 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)125,36725
Polymers122,8692
Non-polymers2,49723
Water3,909217
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A: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,71115
Polymers61,4351
Non-polymers1,27714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,65510
Polymers61,4351
Non-polymers1,2219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-11 kcal/mol
Surface area42460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.638, 105.629, 207.439
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: 61434.707 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, 240 molecules

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


Mass: 92.094 Da / Num. of mol.: 15 / 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-0P5 / 4-{4-[(1H-benzimidazol-2-ylmethyl)amino]-6-(2-chloro-4-methoxyphenoxy)pyrimidin-2-yl}piperazin-2-one


Mass: 479.919 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22ClN7O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.86 Å3/Da / Density % sol: 68.16 %
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: Oct 31, 2010
RadiationMonochromator: VariMax HF (Osmic) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 42959 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.173 / Net I/σ(I): 5.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.9-34.30.6911100
3-3.124.30.5641100
3.12-3.274.30.4311100
3.27-3.444.30.3291100
3.44-3.654.30.2291100
3.65-3.944.30.1751100
3.94-4.334.30.1391100
4.33-4.964.30.111100
4.96-6.244.40.1231100
6.24-504.40.064198.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.1 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.9 Å39.35 Å
Translation2.9 Å39.35 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: 2.901→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.89 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 24.77 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.702 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24331 2154 5 %RANDOM
Rwork0.1895 ---
obs0.19216 40543 99.38 %-
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: 36.866 Å2
Baniso -1Baniso -2Baniso -3
1-5.03 Å20 Å20 Å2
2---2.04 Å20 Å2
3----2.99 Å2
Refinement stepCycle: LAST / Resolution: 2.901→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8361 0 158 217 8736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.028727
X-RAY DIFFRACTIONr_bond_other_d0.0010.025986
X-RAY DIFFRACTIONr_angle_refined_deg1.131.9711827
X-RAY DIFFRACTIONr_angle_other_deg0.822314503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54251039
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66823.484399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.621151436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.241558
X-RAY DIFFRACTIONr_chiral_restr0.0620.21302
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219536
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021829
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: 2.901→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 129 -
Rwork0.29 2725 -
obs--99.65 %
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)
10.72120.54730.29780.81860.31940.6677-0.0105-0.03310.01860.0686-0.001-0.02830.0249-0.05490.01150.16810.0123-0.03490.0572-0.01520.0943-2.09413.39853.596
20.80170.59690.56770.5740.46171.1235-0.0224-0.01190.1062-0.03280.00540.0914-0.0135-0.11410.0170.1216-0.02-0.01990.1102-0.02260.1223-25.986-5.40635.561
30.292-0.0320.70336.8703-1.08461.90240.0944-0.0309-0.04890.38860.11790.7540.2426-0.1022-0.21230.1741-0.04540.0430.02820.01780.0955-30.898-11.99139.503
40.67020.39850.57810.25010.33610.8501-0.08120.03930.0339-0.01810.0427-0.0019-0.10880.01430.03850.1965-0.0031-0.03030.09540.00490.0797-32.135-13.598-10.902
519.68490.08067.17770.5360.05572.6192-0.25453.0415-0.25470.22920.2946-0.2896-0.13011.1166-0.04010.68810.10750.20720.5563-0.10930.3423-61.5-18.458-10.091
61.27930.69450.32010.37980.1721.70460.0044-0.0398-0.0412-0.0114-0.0126-0.0104-0.0281-0.12660.00820.15660.0072-0.0210.05650.01660.1198-38.384-22.884-5.147
71.29630.38580.83360.6990.17911.1127-0.1345-0.06390.1725-0.04030.00090.129-0.1432-0.03210.13360.2035-0.0039-0.05720.0532-0.02380.092-17.3594.82310.536
86.0407-1.01510.39240.61450.38730.5873-0.02680.3690.1642-0.20210.1122-0.11-0.12250.2322-0.08540.1785-0.07270.03170.1291-0.02370.0202-6.6763.9515.683
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A239 - 538
2X-RAY DIFFRACTION2A539 - 736
3X-RAY DIFFRACTION3A737 - 770
4X-RAY DIFFRACTION4B-4 - 360
5X-RAY DIFFRACTION5B361 - 376
6X-RAY DIFFRACTION6B398 - 542
7X-RAY DIFFRACTION7B543 - 731
8X-RAY DIFFRACTION8B732 - 767

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