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- PDB-7wpn: Methionyl-tRNA synthetase from Staphylococcus aureus complexed wi... -

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Basic information

Entry
Database: PDB / ID: 7wpn
TitleMethionyl-tRNA synthetase from Staphylococcus aureus complexed with a phenylbenzimidazole inhibitor and ATP
ComponentsMethionine--tRNA ligase
KeywordsLIGASE/INHIBITOR / LIGASE-INHIBITOR COMPLEX
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 / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / tRNA-binding domain / Putative tRNA binding domain / 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 / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / 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
Chem-29I / ACETIC ACID / ADENOSINE-5'-TRIPHOSPHATE / Methionine--tRNA ligase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYi, J. / Cai, Z. / Qiu, H. / Lu, F. / Chen, B. / Luo, Z. / Gu, Q. / Xu, J. / Zhou, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177140 China
National Natural Science Foundation of China (NSFC)81773636 China
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Fragment screening and structural analyses highlight the ATP-assisted ligand binding for inhibitor discovery against type 1 methionyl-tRNA synthetase.
Authors: Yi, J. / Cai, Z. / Qiu, H. / Lu, F. / Luo, Z. / Chen, B. / Gu, Q. / Xu, J. / Zhou, H.
History
DepositionJan 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)62,3935
Polymers61,1041
Non-polymers1,2894
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-2 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.487, 72.053, 115.488
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 61103.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Strain: COL / Gene: metG / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HII6, methionine-tRNA ligase

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Non-polymers , 5 types, 32 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-29I / (phenylmethyl) N-[(2R)-2-[2-(4-bromanyl-3-oxidanyl-phenyl)-5-(methylcarbamoyl)benzimidazol-1-yl]-2-(3,4-dimethoxyphenyl)ethyl]carbamate


Mass: 659.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H31BrN4O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Sodium cacodylate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: May 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→61.13 Å / Num. obs: 20367 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.6
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2082 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WPM

7wpm


Resolution: 2.4→61.13 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.879 / SU B: 9.511 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.574 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2593 1056 5.2 %RANDOM
Rwork0.2167 ---
obs0.2189 19264 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.24 Å2 / Biso mean: 21.865 Å2 / Biso min: 7.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--1.32 Å2-0 Å2
3----1.35 Å2
Refinement stepCycle: final / Resolution: 2.4→61.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3849 0 83 28 3960
Biso mean--29.47 17.31 -
Num. residues----478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194048
X-RAY DIFFRACTIONr_bond_other_d0.0020.023633
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9425504
X-RAY DIFFRACTIONr_angle_other_deg0.93938419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3065478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08224.286189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65315659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5371518
X-RAY DIFFRACTIONr_chiral_restr0.2430.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214679
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02847
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 83 -
Rwork0.266 1375 -
all-1458 -
obs--99.59 %

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