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

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Basic information

Entry
Database: PDB / ID: 6spp
TitleStructure of the Escherichia coli methionyl-tRNA synthetase variant VI298
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 / metal ion binding / membrane / cytosol / cytoplasm
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
CITRIC ACID / Methionine--tRNA ligase / Methionine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)65,2865
Polymers64,7441
Non-polymers5424
Water12,304683
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint0 kcal/mol
Surface area22780 Å2
Unit cell
Length a, b, c (Å)78.510, 45.530, 86.310
Angle α, β, γ (deg.)90.000, 107.380, 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

#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, BvCmsKSP058_01266, BvCmsNSP007_01600, ED648_21370, UN91_27160
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0F3U9S7, UniProt: P00959*PLUS, methionine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.37 Å3/Da / Density % sol: 48.07 %
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: Mar 23, 2019
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.49→38.91 Å / Num. obs: 93868 / % possible obs: 99.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 19.44 Å2 / CC1/2: 0.998 / Rsym value: 0.076 / Net I/σ(I): 11.2
Reflection shellResolution: 1.49→1.59 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 14735 / CC1/2: 0.613 / Rsym value: 0.964 / % possible all: 99.1

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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: 1.49→38.9 Å / SU ML: 0.1808 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.2613
Details: Refinement was performed using explicit riding hydrogen atoms generated in phenix.
RfactorNum. reflection% reflection
Rfree0.1767 4727 5.04 %
Rwork0.1338 --
obs0.136 93868 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.64 Å2
Refinement stepCycle: LAST / Resolution: 1.49→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 33 683 5092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814855
X-RAY DIFFRACTIONf_angle_d0.97666617
X-RAY DIFFRACTIONf_chiral_restr0.0739684
X-RAY DIFFRACTIONf_plane_restr0.0056876
X-RAY DIFFRACTIONf_dihedral_angle_d25.20681816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.34071400.28212699X-RAY DIFFRACTION89.33
1.51-1.530.32061350.2542923X-RAY DIFFRACTION99.51
1.53-1.550.31221570.23782956X-RAY DIFFRACTION99.52
1.55-1.570.26131650.21282997X-RAY DIFFRACTION99.37
1.57-1.590.27251570.20892923X-RAY DIFFRACTION99.61
1.59-1.610.28061600.2012947X-RAY DIFFRACTION99.55
1.61-1.630.27361510.18643006X-RAY DIFFRACTION99.68
1.63-1.660.24731600.17412939X-RAY DIFFRACTION99.74
1.66-1.680.22531750.17252985X-RAY DIFFRACTION99.72
1.68-1.710.24041310.16952975X-RAY DIFFRACTION99.62
1.71-1.740.2351580.17172963X-RAY DIFFRACTION99.55
1.74-1.770.2251570.152937X-RAY DIFFRACTION99.52
1.77-1.810.21321580.1422974X-RAY DIFFRACTION99.68
1.81-1.840.22911650.14012968X-RAY DIFFRACTION99.46
1.84-1.880.1911470.12852973X-RAY DIFFRACTION99.36
1.88-1.930.17361590.12692942X-RAY DIFFRACTION99.23
1.93-1.980.16821520.12022981X-RAY DIFFRACTION99.65
1.98-2.030.15091460.11922968X-RAY DIFFRACTION99.52
2.03-2.090.1881590.11822987X-RAY DIFFRACTION99.56
2.09-2.160.17011480.11973013X-RAY DIFFRACTION99.65
2.16-2.230.16771640.11842938X-RAY DIFFRACTION99.61
2.23-2.320.17041510.11812995X-RAY DIFFRACTION99.65
2.32-2.430.15991530.11782994X-RAY DIFFRACTION99.71
2.43-2.560.17671840.11922989X-RAY DIFFRACTION99.91
2.56-2.720.18031700.12173002X-RAY DIFFRACTION99.87
2.72-2.930.16961750.12512990X-RAY DIFFRACTION99.94
2.93-3.220.16421630.12353005X-RAY DIFFRACTION99.91
3.22-3.690.13581540.11553017X-RAY DIFFRACTION99.91
3.69-4.640.12741730.1113049X-RAY DIFFRACTION99.69
4.64-38.90.18611600.16723106X-RAY DIFFRACTION98.7

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