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- PDB-6spo: Structure of the Escherichia coli methionyl-tRNA synthetase compl... -

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Basic information

Entry
Database: PDB / ID: 6spo
TitleStructure of the Escherichia coli methionyl-tRNA synthetase complexed with 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 / 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 / Methionine--tRNA ligase / Methionine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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

Downloads & links

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Assembly

Deposited unit
A: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4137
Polymers64,7301
Non-polymers6836
Water13,439746
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint1 kcal/mol
Surface area22690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.290, 45.190, 85.890
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: 64730.008 Da / Num. of mol.: 1 / Mutation: Truncated after residue 547; His-tagged
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

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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-CIT / CITRIC ACID


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


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


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 746 / 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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 281 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 PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2018
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.2→33.1 Å / Num. obs: 178894 / % possible obs: 99 % / Redundancy: 6.4 % / Biso Wilson estimate: 13.44 Å2 / CC1/2: 0.998 / Rsym value: 0.105 / Net I/σ(I): 10
Reflection shellResolution: 1.2→1.27 Å / Mean I/σ(I) obs: 1.11 / Num. unique obs: 29243 / CC1/2: 0.326 / Rsym value: 1.638 / % possible all: 94.8

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Processing

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

1qqt


Resolution: 1.2→33.05 Å / SU ML: 0.1557 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.1559
Details: Refinement was performed using explicit riding hydrogen atoms generated in phenix.
RfactorNum. reflection% reflection
Rfree0.1673 8997 5.03 %
Rwork0.1364 --
obs0.138 178894 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.25 Å2
Refinement stepCycle: LAST / Resolution: 1.2→33.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 41 746 5163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764820
X-RAY DIFFRACTIONf_angle_d0.94946566
X-RAY DIFFRACTIONf_chiral_restr0.159687
X-RAY DIFFRACTIONf_plane_restr0.006863
X-RAY DIFFRACTIONf_dihedral_angle_d23.76341836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.35372660.32764976X-RAY DIFFRACTION88.12
1.21-1.230.30073320.26835679X-RAY DIFFRACTION99.93
1.23-1.240.30842860.26285622X-RAY DIFFRACTION100
1.24-1.260.28773120.25395688X-RAY DIFFRACTION100
1.26-1.270.29192760.25475661X-RAY DIFFRACTION99.98
1.27-1.290.31393130.25235666X-RAY DIFFRACTION99.92
1.29-1.310.30742930.25315643X-RAY DIFFRACTION99.9
1.31-1.330.27033210.25485687X-RAY DIFFRACTION99.78
1.33-1.350.27423100.25185602X-RAY DIFFRACTION99.97
1.35-1.370.2672860.24465699X-RAY DIFFRACTION99.87
1.37-1.40.25492770.24915631X-RAY DIFFRACTION99.92
1.4-1.420.28462840.24945681X-RAY DIFFRACTION99.77
1.42-1.450.29573130.27595676X-RAY DIFFRACTION99.82
1.45-1.480.32533160.26895633X-RAY DIFFRACTION99.8
1.48-1.510.20752610.19125722X-RAY DIFFRACTION99.7
1.51-1.550.20432860.15335624X-RAY DIFFRACTION99.63
1.55-1.580.15923110.12195625X-RAY DIFFRACTION99.41
1.58-1.630.16772950.11245726X-RAY DIFFRACTION99.92
1.63-1.670.14443210.10295671X-RAY DIFFRACTION99.97
1.67-1.730.1442770.09985677X-RAY DIFFRACTION99.93
1.73-1.790.14593070.09555693X-RAY DIFFRACTION100
1.79-1.860.13012980.09655693X-RAY DIFFRACTION99.98
1.86-1.950.12472950.09455711X-RAY DIFFRACTION99.93
1.95-2.050.13143030.09585708X-RAY DIFFRACTION99.88
2.05-2.180.13572940.09745684X-RAY DIFFRACTION99.67
2.18-2.350.12882970.10275705X-RAY DIFFRACTION99.88
2.35-2.580.13693160.1065710X-RAY DIFFRACTION99.8
2.58-2.960.13523350.11565739X-RAY DIFFRACTION100
2.96-3.720.14343030.11365778X-RAY DIFFRACTION99.7
3.72-33.050.15353130.13425887X-RAY DIFFRACTION99.45

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