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- PDB-4eg8: Trypanosoma brucei methionyl-tRNA synthetase in complex with comp... -

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Basic information

Entry
Database: PDB / ID: 4eg8
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with compound Chem 89
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
2-aminoquinolin-8-ol / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.596 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 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, putative
B: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,41129
Polymers122,8692
Non-polymers2,54227
Water8,305461
1
A: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,81716
Polymers61,4351
Non-polymers1,38315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,59413
Polymers61,4351
Non-polymers1,15912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.861, 105.727, 206.649
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 237-773 / 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 , 5 types, 488 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.: 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-0P6 / 2-aminoquinolin-8-ol


Mass: 160.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8N2O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 68.51 %
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: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 17, 2011
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.596→50 Å / Num. obs: 60150 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 5.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.596-2.6450.756199.6
2.64-2.6950.7241100
2.69-2.7450.6131100
2.74-2.85.10.5571100
2.8-2.8650.511100
2.86-2.9350.4361100
2.93-35.10.3721100
3-3.0850.3091100
3.08-3.1750.2851100
3.17-3.2850.2321100
3.28-3.3950.21100
3.39-3.5350.161100
3.53-3.6950.1271100
3.69-3.8850.1031100
3.88-4.1350.0891100
4.13-4.4550.0781100
4.45-4.8950.0741100
4.89-5.650.0751100
5.6-7.054.90.079199.9
7.05-504.70.035199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.55 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.6 Å45.3 Å
Translation2.6 Å45.3 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 4EG1

4eg1


Resolution: 2.596→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 15.296 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22369 3022 5 %RANDOM
Rwork0.17681 ---
obs0.17915 56834 99.3 %-
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: 37.592 Å2
Baniso -1Baniso -2Baniso -3
1-3.64 Å20 Å20 Å2
2---1.86 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.596→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8510 0 161 461 9132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.028905
X-RAY DIFFRACTIONr_bond_other_d0.0010.026127
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.96812065
X-RAY DIFFRACTIONr_angle_other_deg0.832314872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50751069
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78823.433402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.281151467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2361559
X-RAY DIFFRACTIONr_chiral_restr0.0630.21337
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021869
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: 2.596→2.663 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 216 -
Rwork0.266 3737 -
obs--96.23 %
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)
11.3350.9632-0.66591.7721-0.65221.1296-0.0075-0.0859-0.08530.1621-0.0278-0.01870.0410.07280.03530.20730.01990.05860.11120.01120.13572.1827-13.215553.2495
21.8430.6765-0.50221.76-0.40432.2272-0.0611-0.1656-0.32910.0348-0.0565-0.28320.09470.33040.11760.09940.01220.03620.18610.00660.169527.41775.005135.4013
30.2430.6314-0.35916.8208-0.08422.8430.069-0.2182-0.02350.2887-0.033-1.129-0.0960.6039-0.0360.085-0.0598-0.0190.2802-0.07050.239329.784312.625839.7301
41.41380.6214-0.70811.0001-0.44241.4303-0.1190.1561-0.0676-0.18590.0688-0.11830.10510.01130.05020.1508-0.01420.01110.1753-0.00220.10233.235313.8228-10.9294
51.9724-1.30470.46056.9210.55420.43070.47930.0208-0.73270.2687-0.0368-0.71860.39440.3607-0.44250.5860.2643-0.29780.6994-0.05490.80162.716615.4602-10.053
61.56210.6352-0.77111.3384-0.23611.8893-0.0066-0.05720.0233-0.0854-0.00540.0157-0.06520.11490.0120.1189-0.01640.02020.15930.00810.129637.920321.887-4.3263
71.96350.5424-0.82281.3354-0.25471.6878-0.15010.0028-0.2839-0.0590.0071-0.11360.3281-0.04670.1430.1707-0.01910.02620.12870.01770.135516.3134-4.652610.6038
86.3146-1.34970.04250.4114-0.47832.01810.11720.3773-0.9916-0.1517-0.04060.23380.4314-0.288-0.07650.1887-0.0637-0.02220.1593-0.03870.23037.5914-4.79576.3522
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 545
2X-RAY DIFFRACTION2A546 - 735
3X-RAY DIFFRACTION3A736 - 768
4X-RAY DIFFRACTION4B-4 - 362
5X-RAY DIFFRACTION5B363 - 403
6X-RAY DIFFRACTION6B404 - 548
7X-RAY DIFFRACTION7B549 - 735
8X-RAY DIFFRACTION8B736 - 767

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