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- PDB-4eg1: Trypanosoma brucei methionyl-tRNA synthetase in complex with subs... -

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Basic information

Entry
Database: PDB / ID: 4eg1
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with substrate Methionine
ComponentsMethionyl-tRNA synthetase, putative
KeywordsLIGASE / aminoacyl-tRNA synthetase / aaRS / MetRS / parasite / protein-inhibitor complex / Rossmann-fold / translation / nucleotide binding / Rossmann Fold / tRNA binding ATP binding
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
METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 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 17, 2012Group: Other
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Nov 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 1.4Sep 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 1.5Nov 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)124,27316
Polymers122,8692
Non-polymers1,40414
Water1,45981
1
A: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2299
Polymers61,4351
Non-polymers7948
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0447
Polymers61,4351
Non-polymers6106
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.037, 105.935, 207.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Methionyl-tRNA synthetase, putative


Mass: 61434.707 Da / Num. of mol.: 2 / Fragment: RESIDUES 235-771 / 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
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
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: 3.8 Å3/Da / Density % sol: 67.61 %
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 8, 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: 42449 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.9-35.70.7261100
3-3.125.70.5421100
3.12-3.275.70.4191100
3.27-3.445.80.31100
3.44-3.655.90.2071100
3.65-3.946.10.1611100
3.94-4.336.30.1221100
4.33-4.966.50.1021100
4.96-6.246.70.11100
6.24-506.70.054198.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.13 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å43.94 Å
Translation2.8 Å43.94 Å

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Processing

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

3kfl


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 33.878 / SU ML: 0.296 / SU R Cruickshank DPI: 0.7873 / Cross valid method: THROUGHOUT / ESU R: 0.787 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25393 2124 5 %RANDOM
Rwork0.20851 ---
obs0.21078 39977 99.37 %-
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: 43.232 Å2
Baniso -1Baniso -2Baniso -3
1-10.72 Å20 Å20 Å2
2---5.68 Å20 Å2
3----5.05 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8495 0 90 81 8666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.028791
X-RAY DIFFRACTIONr_bond_other_d0.0020.026025
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.96311923
X-RAY DIFFRACTIONr_angle_other_deg0.821314631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88751059
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01423.516401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.719151453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.251558
X-RAY DIFFRACTIONr_chiral_restr0.060.21318
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219655
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021847
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: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 147 -
Rwork0.315 2654 -
obs--99.47 %
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)
10.82660.4454-0.52571.7503-0.68420.57960.00180.0120.06460.23020.02740.0670.0870.0789-0.02920.22860.05170.07780.1699-0.01410.1399-40.1558-15.157453.2555
20.67260.4761-0.74680.4709-0.53271.83480.10420.0886-0.10880.1655-0.0469-0.137-0.04870.3442-0.05740.095-0.0115-0.02280.30090.00440.2529-17.0573.671334.3791
30.2902-0.986-0.18693.48690.97461.2017-0.0032-0.06530.03040.03480.2684-0.1628-0.23870.2011-0.26520.2643-0.12070.15630.1606-0.06720.1937-14.129713.039838.4131
40.9240.3238-0.71830.8565-0.05211.6326-0.07820.0943-0.0711-0.3090.11290.0535-0.0301-0.0869-0.03470.1287-0.02750.02790.24160.03180.1904-12.964514.6009-11.7335
54.6029-5.10793.60866.0595-3.063712.87580.1438-0.3964-0.12920.06190.12390.10531.0243-0.1567-0.26770.1664-0.1585-0.00020.36620.0440.318111.822812.9814-6.9733
61.94620.8538-0.48491.565-0.22421.8723-0.043-0.04730.0624-0.23690.1268-0.0453-0.13950.102-0.08380.0588-0.0110.03130.14730.01870.1599-7.683223.6708-6.774
70.50780.3848-0.64230.989-0.88431.6318-0.1423-0.0792-0.0763-0.15580.0125-0.11540.37310.00560.12980.0925-0.0030.04680.23370.00050.1732-26.2389-3.74619.2284
83.62240.76440.03681.1784-0.92060.855-0.11640.1487-0.2436-0.17160.32750.17320.1121-0.2972-0.21110.1179-0.0293-0.00120.28250.02830.2391-36.9665-5.17445.1878
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A239 - 537
2X-RAY DIFFRACTION2A538 - 735
3X-RAY DIFFRACTION3A736 - 767
4X-RAY DIFFRACTION4B-4 - 367
5X-RAY DIFFRACTION5B368 - 395
6X-RAY DIFFRACTION6B396 - 533
7X-RAY DIFFRACTION7B534 - 730
8X-RAY DIFFRACTION8B731 - 768

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