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- PDB-8bru: Escherichia coli methionyl-tRNA synthetase mutant L13M,I297C -

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Basic information

Entry
Database: PDB / ID: 8bru
TitleEscherichia coli methionyl-tRNA synthetase mutant L13M,I297C
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
CITRIC ACID / Methionine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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
CitationJournal: 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.
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

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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)65,1884
Polymers64,7381
Non-polymers4503
Water10,935607
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)78.310, 45.080, 86.170
Angle α, β, γ (deg.)90.000, 107.540, 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: 64738.023 Da / Num. of mol.: 1 / Mutation: L13M, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.08M ammonium citrate, 30 mM 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: 1.54→49 Å / Num. obs: 83751 / % possible obs: 98.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 23.09 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.079 / Rsym value: 0.073 / Net I/σ(I): 12.8
Reflection shellResolution: 1.54→1.64 Å / Mean I/σ(I) obs: 1.13 / Num. unique obs: 12534 / CC1/2: 0.636 / Rsym value: 1.16

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→49 Å / SU ML: 0.1893 / Cross valid method: FREE R-VALUE / Phase error: 18.3021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1806 4234 5.07 %
Rwork0.1442 79336 -
obs0.1461 83570 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.59 Å2
Refinement stepCycle: LAST / Resolution: 1.55→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4373 0 27 607 5007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00684509
X-RAY DIFFRACTIONf_angle_d0.83936104
X-RAY DIFFRACTIONf_chiral_restr0.0493636
X-RAY DIFFRACTIONf_plane_restr0.0075798
X-RAY DIFFRACTIONf_dihedral_angle_d15.02061655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.560.37641040.31781982X-RAY DIFFRACTION74.58
1.56-1.580.30421500.24422595X-RAY DIFFRACTION99.96
1.58-1.60.3031460.22282703X-RAY DIFFRACTION99.89
1.6-1.620.28011280.21042642X-RAY DIFFRACTION99.96
1.62-1.640.25541440.19852620X-RAY DIFFRACTION99.89
1.64-1.670.27781500.19092661X-RAY DIFFRACTION100
1.67-1.690.24651300.19222627X-RAY DIFFRACTION99.86
1.69-1.710.27251280.21212664X-RAY DIFFRACTION99.93
1.71-1.740.31351450.22022691X-RAY DIFFRACTION99.96
1.74-1.770.24441360.20212656X-RAY DIFFRACTION100
1.77-1.80.23541540.17822653X-RAY DIFFRACTION99.93
1.8-1.830.26981470.16192615X-RAY DIFFRACTION100
1.83-1.870.2081320.1412694X-RAY DIFFRACTION100
1.87-1.910.19471370.12622620X-RAY DIFFRACTION100
1.91-1.950.16771350.12492689X-RAY DIFFRACTION99.93
1.95-1.990.18431310.1212638X-RAY DIFFRACTION99.89
1.99-2.040.19091490.13132664X-RAY DIFFRACTION99.82
2.04-2.10.1721320.12912664X-RAY DIFFRACTION100
2.1-2.160.17641320.12882692X-RAY DIFFRACTION100
2.16-2.230.15561560.1122665X-RAY DIFFRACTION99.96
2.23-2.310.17031320.11542644X-RAY DIFFRACTION99.93
2.31-2.40.15941320.11552676X-RAY DIFFRACTION100
2.4-2.510.16751540.12262693X-RAY DIFFRACTION99.82
2.51-2.640.17361630.12722634X-RAY DIFFRACTION99.82
2.64-2.810.16431550.13532675X-RAY DIFFRACTION99.93
2.81-3.030.18521450.14542685X-RAY DIFFRACTION99.89
3.03-3.330.17671580.14492659X-RAY DIFFRACTION99.89
3.33-3.810.14871350.13152701X-RAY DIFFRACTION99.72
3.81-4.80.13381460.12572728X-RAY DIFFRACTION100
4.8-48.470.19791480.18332806X-RAY DIFFRACTION99.66

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