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- PDB-8xm3: Methionyl-tRNA synthetase from Staphylococcus aureus complexed wi... -

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Basic information

Entry
Database: PDB / ID: 8xm3
TitleMethionyl-tRNA synthetase from Staphylococcus aureus complexed with a chlorhexidine derivative and ATP
ComponentsMethionine--tRNA ligase
KeywordsLIGASE / MetRS / methionyl-tRNA synthetase
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
Methionyl-tRNA synthetase, beta subunit, C-terminal / Methionine-tRNA synthetase, type 2 / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / tRNA-binding domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Putative tRNA binding domain / Anticodon-binding domain of tRNA ligase / tRNA-binding domain profile. ...Methionyl-tRNA synthetase, beta subunit, C-terminal / Methionine-tRNA synthetase, type 2 / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / tRNA-binding domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Putative tRNA binding domain / Anticodon-binding domain of tRNA ligase / 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
: / ADENOSINE-5'-TRIPHOSPHATE / Methionine--tRNA ligase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsLu, F. / Xia, K. / Yi, J. / Chen, B. / Luo, Z. / Xu, J. / Gu, Q. / Zhou, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2217714 China
National Natural Science Foundation of China (NSFC)22207133 China
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Biochemical and structural characterization of chlorhexidine as an ATP-assisted inhibitor against type 1 methionyl-tRNA synthetase from Gram-positive bacteria.
Authors: Lu, F. / Xia, K. / Su, J. / Yi, J. / Luo, Z. / Xu, J. / Gu, Q. / Chen, B. / Zhou, H.
History
DepositionDec 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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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)62,5664
Polymers61,1041
Non-polymers1,4623
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.780, 114.780, 79.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 61103.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Gene: metG / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HII6, methionine-tRNA ligase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-A1LV5 / 1-(4-chlorophenyl)-3-[~{N}-[4-[[~{N}-[~{N}-(4-chlorophenyl)carbamimidoyl]carbamimidoyl]amino]butyl]carbamimidoyl]guanidine


Mass: 477.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26Cl2N10 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium cacodylate pH 6.7, 16% w/v PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→62.23 Å / Num. obs: 39246 / % possible obs: 84.7 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.027 / Rrim(I) all: 0.085 / Χ2: 0.96 / Net I/σ(I): 20.2 / Num. measured all: 391195
Reflection shellResolution: 1.92→2.03 Å / % possible obs: 73.1 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.848 / Num. measured all: 49241 / Num. unique obs: 4896 / CC1/2: 0.844 / Rpim(I) all: 0.278 / Rrim(I) all: 0.893 / Χ2: 0.89 / Net I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PHASERphasing
PDB_EXTRACTdata extraction
autoPROCdata scaling
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→62.23 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.038 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22075 1951 5 %RANDOM
Rwork0.19113 ---
obs0.1926 37268 84.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.149 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.02 Å2-0 Å2
2---0.05 Å20 Å2
3---0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.92→62.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4201 0 95 212 4508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194445
X-RAY DIFFRACTIONr_bond_other_d0.0070.023979
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.9676041
X-RAY DIFFRACTIONr_angle_other_deg0.96139242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4985518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26624.593209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95215732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.521518
X-RAY DIFFRACTIONr_chiral_restr0.0670.2637
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025049
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02931
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7782.972075
X-RAY DIFFRACTIONr_mcbond_other0.7772.9692074
X-RAY DIFFRACTIONr_mcangle_it1.374.452592
X-RAY DIFFRACTIONr_mcangle_other1.3694.4512593
X-RAY DIFFRACTIONr_scbond_it0.6853.0342366
X-RAY DIFFRACTIONr_scbond_other0.6853.0352367
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.224.5113448
X-RAY DIFFRACTIONr_long_range_B_refined2.79434.0355047
X-RAY DIFFRACTIONr_long_range_B_other2.67733.935010
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.925→1.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 106 -
Rwork0.274 1479 -
obs--46.77 %
Refinement TLS params.Method: refined / Origin x: -11.0309 Å / Origin y: 46.3746 Å / Origin z: 10.9624 Å
111213212223313233
T0.0202 Å2-0.0001 Å2-0.0088 Å2-0.0412 Å20.0062 Å2--0.0122 Å2
L0.2088 °2-0.1844 °20.0891 °2-0.2566 °2-0.1325 °2--0.0721 °2
S-0.0041 Å °-0.0037 Å °-0.013 Å °0.0145 Å °-0.0095 Å °-0.0184 Å °-0.0147 Å °0.0003 Å °0.0136 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 115
2X-RAY DIFFRACTION1A116 - 152
3X-RAY DIFFRACTION1A153 - 266
4X-RAY DIFFRACTION1A267 - 318
5X-RAY DIFFRACTION1A319 - 362
6X-RAY DIFFRACTION1A363 - 520

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