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- PDB-6spr: Structure of the Escherichia coli methionyl-tRNA synthetase varia... -

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Basic information

Entry
Database: PDB / ID: 6spr
TitleStructure of the Escherichia coli methionyl-tRNA synthetase variant VI298 complexed with beta-methionine
ComponentsMethionine--tRNA ligase
KeywordsTRANSLATION / tRNA aminoacylation
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / protein homodimerization activity / zinc ion binding / ATP binding / membrane / cytosol
Similarity search - Function
Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase, beta subunit, C-terminal / 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 / tRNA-binding domain ...Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase, beta subunit, C-terminal / 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 / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / 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 / Nucleic acid-binding, OB-fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(3R)-3-amino-5-(methylsulfanyl)pentanoic acid / CITRIC ACID / Methionine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsNigro, G. / Schmitt, E. / Mechulam, Y.
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Use of beta3-methionine as an amino acid substrate of Escherichia coli methionyl-tRNA synthetase.
Authors: Nigro, G. / Bourcier, S. / Lazennec-Schurdevin, C. / Schmitt, E. / Marliere, P. / Mechulam, Y.
History
DepositionSep 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.title / _citation.year
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7259
Polymers64,7441
Non-polymers9818
Water13,403744
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-0 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.310, 45.110, 86.210
Angle α, β, γ (deg.)90.000, 107.390, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 64744.031 Da / Num. of mol.: 1 / Mutation: Truncated after residue 547; His-tagged ; VI298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: metG, b2114, JW2101 / Production host: Escherichia coli (E. coli) / References: UniProt: P00959, methionine-tRNA ligase

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Non-polymers , 5 types, 752 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-B3M / (3R)-3-amino-5-(methylsulfanyl)pentanoic acid


Type: L-peptide linking / Mass: 163.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 744 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 1.08 M ammonium citrate, 10 mM potassium phosphate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.48→48.6 Å / Num. obs: 96417 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 16.66 Å2 / CC1/2: 0.998 / Rsym value: 0.117 / Net I/σ(I): 9.2
Reflection shellResolution: 1.48→1.57 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 15234 / CC1/2: 0.597 / Rsym value: 1.03

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QQT

1qqt


Resolution: 1.48→48.56 Å / SU ML: 0.1737 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.8831
Details: Refinement was performed using explicit riding hydrogen atoms generated in phenix.
RfactorNum. reflection% reflection
Rfree0.1678 4833 5.01 %
Rwork0.131 --
obs0.1329 96417 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.4 Å2
Refinement stepCycle: LAST / Resolution: 1.48→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4377 0 61 744 5182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00794918
X-RAY DIFFRACTIONf_angle_d0.94696691
X-RAY DIFFRACTIONf_chiral_restr0.1503687
X-RAY DIFFRACTIONf_plane_restr0.0056889
X-RAY DIFFRACTIONf_dihedral_angle_d24.76461856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.490.35271280.31922801X-RAY DIFFRACTION91.88
1.49-1.510.37411430.27843071X-RAY DIFFRACTION99.97
1.51-1.530.26551400.23883043X-RAY DIFFRACTION100
1.53-1.550.23591650.21093011X-RAY DIFFRACTION99.94
1.55-1.570.26191590.20343051X-RAY DIFFRACTION99.97
1.57-1.590.25761810.19043019X-RAY DIFFRACTION99.97
1.59-1.610.24891590.16873075X-RAY DIFFRACTION99.97
1.61-1.640.18481630.15753015X-RAY DIFFRACTION99.97
1.64-1.660.22881530.1553076X-RAY DIFFRACTION99.97
1.66-1.690.20871610.15582984X-RAY DIFFRACTION99.97
1.69-1.720.21591500.14613065X-RAY DIFFRACTION99.97
1.72-1.750.19411690.14633062X-RAY DIFFRACTION99.97
1.75-1.790.19981600.13833061X-RAY DIFFRACTION99.94
1.79-1.820.18511730.1393031X-RAY DIFFRACTION99.94
1.82-1.860.19661560.14463032X-RAY DIFFRACTION99.97
1.86-1.90.18021530.14133050X-RAY DIFFRACTION99.91
1.9-1.950.19321610.13553096X-RAY DIFFRACTION99.97
1.95-20.15551510.11543028X-RAY DIFFRACTION100
2-2.060.15281760.11033072X-RAY DIFFRACTION99.97
2.06-2.130.15081460.10743035X-RAY DIFFRACTION100
2.13-2.210.15471610.10533077X-RAY DIFFRACTION100
2.21-2.290.14851650.10773054X-RAY DIFFRACTION100
2.29-2.40.1561530.10783081X-RAY DIFFRACTION100
2.4-2.530.15691780.11623067X-RAY DIFFRACTION100
2.53-2.680.1441790.11543045X-RAY DIFFRACTION99.97
2.68-2.890.15321840.11943053X-RAY DIFFRACTION100
2.89-3.180.16121610.11853091X-RAY DIFFRACTION99.94
3.18-3.640.141610.11393109X-RAY DIFFRACTION100
3.64-4.590.12961770.10663119X-RAY DIFFRACTION100
4.59-48.560.17621670.16553210X-RAY DIFFRACTION99.91

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