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- PDB-6wqi: Xanthomonas citri Methionyl-tRNA synthetase (apo) -

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Basic information

Entry
Database: PDB / ID: 6wqi
TitleXanthomonas citri Methionyl-tRNA synthetase (apo)
ComponentsMethionine--tRNA ligase
KeywordsLIGASE / Ligand-free / apo / tRNA / aminoacylation
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / ATP binding / metal ion binding / 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 / 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
Methionine--tRNA ligase
Similarity search - Component
Biological speciesXanthomonas citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsMercaldi, G.F. / Benedetti, C.E.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)11/20468-1 Brazil
Sao Paulo Research Foundation (FAPESP)18/08535-4 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)465440/2014-2 Brazil
Sao Paulo Research Foundation (FAPESP)14/50880-0 Brazil
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Molecular basis for diaryldiamine selectivity and competition with tRNA in a type 2 methionyl-tRNA synthetase from a Gram-negative bacterium.
Authors: Mercaldi, G.F. / Andrade, M.O. / Zanella, J.L. / Cordeiro, A.T. / Benedetti, C.E.
History
DepositionApr 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.3Oct 18, 2023Group: 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
B: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,0044
Polymers154,8742
Non-polymers1312
Water8,971498
1
A: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5022
Polymers77,4371
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5022
Polymers77,4371
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.017, 95.253, 84.080
Angle α, β, γ (deg.)90.000, 90.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 77436.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas citri (bacteria) / Strain: 306 / Gene: metG, metS, XAC1386 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8PMP0, methionine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 1.91 Å3/Da / Density % sol: 35.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl, 28 - 32% PEG4000, 0.2 M MgCl2, 0.45 % Polyvinylpyrrolidone K15
PH range: 7.9 - 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2→47.83 Å / Num. obs: 76238 / % possible obs: 97 % / Redundancy: 3.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.069 / Rrim(I) all: 0.127 / Net I/σ(I): 8.6
Reflection shellResolution: 2→2.04 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.918 / Num. unique obs: 4423 / CC1/2: 0.574 / Rpim(I) all: 0.609 / Rrim(I) all: 1.107 / % possible all: 95

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7 Å47.63 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WQ6

6wq6


Resolution: 2→47.83 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.443 / SU ML: 0.1 / SU R Cruickshank DPI: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.035
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2301 3766 4.9 %RANDOM
Rwork0.185 ---
obs0.1874 72445 94.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.49 Å2 / Biso mean: 32.944 Å2 / Biso min: 19.73 Å2
Baniso -1Baniso -2Baniso -3
1-44.92 Å20 Å29.17 Å2
2---25.19 Å2-0 Å2
3----19.74 Å2
Refinement stepCycle: final / Resolution: 2→47.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8488 0 2 498 8988
Biso mean--33.54 39.88 -
Num. residues----1094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0138713
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177950
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.64111844
X-RAY DIFFRACTIONr_angle_other_deg1.4371.57518368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43851092
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32921.652460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.978151340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2771558
X-RAY DIFFRACTIONr_chiral_restr0.0840.21122
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029940
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021970
LS refinement shellResolution: 1.983→2.035 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 158 -
Rwork0.262 3598 -
all-3756 -
obs--63.22 %

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