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- PDB-6ax8: Mycobacterium tuberculosis methionyl-tRNA synthetase in complex w... -

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Basic information

Entry
Database: PDB / ID: 6ax8
TitleMycobacterium tuberculosis methionyl-tRNA synthetase in complex with methionyl-adenylate
ComponentsMethionine-tRNA ligase
KeywordsLIGASE / synthetase / Ligase-aminoacyl adenylate complex
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ATP binding / plasma membrane / 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 / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / 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-ME8 / Methionine--tRNA ligase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBarros-Alvarez, X. / Hol, W.G.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1 AI084004 and RO1 AI097177 United States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: The crystal structure of the drug target Mycobacterium tuberculosis methionyl-tRNA synthetase in complex with a catalytic intermediate.
Authors: Barros-Alvarez, X. / Turley, S. / Ranade, R.M. / Gillespie, J.R. / Duster, N.A. / Verlinde, C.L.M.J. / Fan, E. / Buckner, F.S. / Hol, W.G.J.
History
DepositionSep 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6372
Polymers58,1581
Non-polymers4781
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20460 Å2
Unit cell
Length a, b, c (Å)196.958, 196.958, 39.177
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Methionine-tRNA ligase / Methionyl-tRNA synthetase / MetRS


Mass: 58158.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: metG, metS, Rv1007c, MTCI237.24 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WFU5, methionine-tRNA ligase
#2: Chemical ChemComp-ME8 / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] (2S)-2-azanyl-4-methylsulfanyl-butanoate / L-methionine-AMP / methionyl-adenylate


Mass: 478.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N6O8PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1-0.2 M ammonium sulfate, 30-34 % PEG 8K, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2015
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→98.48 Å / Num. obs: 17391 / % possible obs: 99.9 % / Redundancy: 5.3 % / Net I/σ(I): 7.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimlessdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→98.48 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.898 / Cross valid method: THROUGHOUT / ESU R: 2.55 / ESU R Free: 0.324 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24602 948 5.5 %RANDOM
Rwork0.23672 ---
obs0.23723 16441 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 59.466 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å2-1.09 Å20 Å2
2---2.17 Å20 Å2
3---7.05 Å2
Refinement stepCycle: 1 / Resolution: 2.6→98.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3980 0 31 38 4049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194117
X-RAY DIFFRACTIONr_bond_other_d00.023794
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9465615
X-RAY DIFFRACTIONr_angle_other_deg3.74738660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6335508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39422.727198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6815605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6071537
X-RAY DIFFRACTIONr_chiral_restr0.0730.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214724
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021026
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_it2.5415.9072035
X-RAY DIFFRACTIONr_mcbond_other2.5415.9082036
X-RAY DIFFRACTIONr_mcangle_it4.1658.8622543
X-RAY DIFFRACTIONr_mcangle_other4.1658.8632543
X-RAY DIFFRACTIONr_scbond_it2.9736.1662082
X-RAY DIFFRACTIONr_scbond_other2.9726.1672083
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0379.153073
X-RAY DIFFRACTIONr_long_range_B_refined7.57547.2224611
X-RAY DIFFRACTIONr_long_range_B_other7.57447.2324612
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 62 -
Rwork0.367 1205 -
obs--99.84 %

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