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- PDB-8brx: Escherichia coli methionyl-tRNA synthetase mutant L13C,I297C comp... -

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Basic information

Entry
Database: PDB / ID: 8brx
TitleEscherichia coli methionyl-tRNA synthetase mutant L13C,I297C complexed with beta-3-methionine
ComponentsMethionine--tRNA ligase
KeywordsTRANSLATION / beta-methionine / aminoacyl-tRNA synthetase / MetRS / tRNA
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 / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. ...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 / 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. / Rossmann-like alpha/beta/alpha sandwich fold / Nucleic acid-binding, OB-fold
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: 1.54 Å
AuthorsSchmitt, E. / Mechulam, Y. / Nigro, G. / Opuu, V. / Lazennec-Schurdevin, C. / Simonson, T.
Funding support France, 2items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS)UMR7654 France
Other governmentUMR7654
Citation
Journal: Protein Sci. / Year: 2023
Title: Redesigning methionyl-tRNA synthetase for beta-methionine activity with adaptive landscape flattening and experiments.
Authors: Opuu, V. / Nigro, G. / Lazennec-Schurdevin, C. / Mechulam, Y. / Schmitt, E. / Simonson, T.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionNov 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
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 / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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)65,3235
Polymers64,7101
Non-polymers6134
Water11,494638
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.660, 45.510, 86.430
Angle α, β, γ (deg.)90.000, 107.510, 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: 64709.977 Da / Num. of mol.: 1 / Mutation: L13C, I297C, E548Stop
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
#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-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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.08 M ammonium citrate, 30mM potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 86690 / % possible obs: 98.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 20.83 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.109 / Rsym value: 0.1 / Net I/σ(I): 14.36
Reflection shellResolution: 1.53→1.63 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.16 / Num. unique obs: 13088 / CC1/2: 0.502 / Rrim(I) all: 1.275 / Rsym value: 1.173 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→41.82 Å / SU ML: 0.2675 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2477
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1983 4381 5.07 %
Rwork0.1647 82016 -
obs0.1664 86397 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.34 Å2
Refinement stepCycle: LAST / Resolution: 1.54→41.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4372 0 37 638 5047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00384647
X-RAY DIFFRACTIONf_angle_d0.63686303
X-RAY DIFFRACTIONf_chiral_restr0.0426650
X-RAY DIFFRACTIONf_plane_restr0.0049827
X-RAY DIFFRACTIONf_dihedral_angle_d14.73931709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.550.5231000.46661833X-RAY DIFFRACTION66.68
1.55-1.570.34151550.34562782X-RAY DIFFRACTION99.76
1.57-1.590.37611480.34322704X-RAY DIFFRACTION99.93
1.59-1.610.35781490.34332745X-RAY DIFFRACTION99.93
1.61-1.630.39271390.31052780X-RAY DIFFRACTION99.76
1.63-1.650.30551480.30392700X-RAY DIFFRACTION99.79
1.65-1.680.35911570.28942758X-RAY DIFFRACTION99.9
1.68-1.70.29321290.28192721X-RAY DIFFRACTION99.79
1.7-1.730.37281360.28372748X-RAY DIFFRACTION99.59
1.73-1.760.32011550.27612755X-RAY DIFFRACTION99.66
1.76-1.790.3371340.27552753X-RAY DIFFRACTION99.65
1.79-1.820.33541600.27372778X-RAY DIFFRACTION99.66
1.82-1.860.32261400.2912738X-RAY DIFFRACTION99.69
1.86-1.890.32671430.30472759X-RAY DIFFRACTION99.79
1.89-1.930.30891440.26362717X-RAY DIFFRACTION99.72
1.93-1.980.22561460.15762778X-RAY DIFFRACTION99.93
1.98-2.030.18061340.13652750X-RAY DIFFRACTION99.83
2.03-2.080.16361510.12422748X-RAY DIFFRACTION99.79
2.08-2.150.17691350.122769X-RAY DIFFRACTION99.93
2.15-2.210.15761490.11552796X-RAY DIFFRACTION99.93
2.21-2.290.18251520.12062743X-RAY DIFFRACTION99.97
2.29-2.390.14831380.12152812X-RAY DIFFRACTION99.86
2.39-2.490.17161570.12692694X-RAY DIFFRACTION99.86
2.49-2.630.171680.12952781X-RAY DIFFRACTION99.9
2.63-2.790.16281560.13562798X-RAY DIFFRACTION99.93
2.79-3.010.15951560.13922755X-RAY DIFFRACTION99.97
3.01-3.310.18821520.14122774X-RAY DIFFRACTION99.93
3.31-3.790.14661480.12792820X-RAY DIFFRACTION99.93
3.79-4.770.1321520.12322823X-RAY DIFFRACTION99.9
4.77-41.820.19921500.17822904X-RAY DIFFRACTION99.54

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