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- PDB-9shc: Structure of Streptococcus pneumoniae methionyl-tRNA synthetase b... -

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Basic information

Entry
Database: PDB / ID: 9shc
TitleStructure of Streptococcus pneumoniae methionyl-tRNA synthetase bound to the sulphamoyl analogue of methionyl-adenylate
ComponentsMethionine--tRNA ligase
KeywordsRNA BINDING PROTEIN / aminoacyl-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 / 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 ...Methionyl-tRNA synthetase, beta subunit, C-terminal / Methionine-tRNA synthetase, type 2 / 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 / Rossmann-like alpha/beta/alpha sandwich fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / Methionine--tRNA ligase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCusack, S. / Fridd, S.
Funding support France, 1items
OrganizationGrant numberCountry
Other government France
CitationJournal: To Be Published
Title: Structure of Streptococcus pneumoniae methionyl-tRNA synthetase bound to the sulphamoyl analogue of methionine-adenylate
Authors: Cusack, S.
History
DepositionAug 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: 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)76,2112
Polymers75,7341
Non-polymers4781
Water86548
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)150.365, 72.888, 78.881
Angle α, β, γ (deg.)90.000, 117.420, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 75733.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal dimerisation domain not visible in the electron density
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: metG, metS, SP_0788 / Production host: Escherichia coli (E. coli) / References: UniProt: P67580, methionine-tRNA ligase
#2: Chemical ChemComp-A1MAL / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methylsulfanyl-butanoyl]sulfamate / sulfamate analog of methionyl adenylate (Met-AMS)


Mass: 477.516 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O7S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: Don't know.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 14, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 31310 / % possible obs: 93.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.2
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.382 / Num. unique obs: 1421

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.101 / SU ML: 0.165 / Cross valid method: FREE R-VALUE / ESU R: 0.279 / ESU R Free: 0.221
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2471 1561 4.986 %
Rwork0.2083 29749 -
all0.21 --
obs-31310 93.09 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.998 Å2
Baniso -1Baniso -2Baniso -3
1--2.847 Å20 Å2-0.929 Å2
2--4.181 Å2-0 Å2
3----0.241 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4032 0 31 48 4111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0124190
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163882
X-RAY DIFFRACTIONr_angle_refined_deg1.0331.8235704
X-RAY DIFFRACTIONr_angle_other_deg0.4071.7498926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0665498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.541524
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.00451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24510681
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.9310204
X-RAY DIFFRACTIONr_chiral_restr0.0560.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024907
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02980
X-RAY DIFFRACTIONr_nbd_refined0.1960.2813
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.23404
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22054
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.21986
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.286
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2590.213
X-RAY DIFFRACTIONr_nbd_other0.0950.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0280.22
X-RAY DIFFRACTIONr_mcbond_it1.8513.9861998
X-RAY DIFFRACTIONr_mcbond_other1.8493.9841997
X-RAY DIFFRACTIONr_mcangle_it3.177.1492494
X-RAY DIFFRACTIONr_mcangle_other3.177.1512495
X-RAY DIFFRACTIONr_scbond_it2.0354.1762192
X-RAY DIFFRACTIONr_scbond_other2.0354.1752193
X-RAY DIFFRACTIONr_scangle_it3.5567.5763210
X-RAY DIFFRACTIONr_scangle_other3.5567.5753211
X-RAY DIFFRACTIONr_lrange_it5.23137.514636
X-RAY DIFFRACTIONr_lrange_other5.22937.5184631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.3590.34510.3011061X-RAY DIFFRACTION49.0733
2.359-2.4230.308940.2841835X-RAY DIFFRACTION80.0747
2.423-2.4930.281170.2651988X-RAY DIFFRACTION89.9188
2.493-2.5690.2851010.2532080X-RAY DIFFRACTION95.826
2.569-2.6520.2871180.2282015X-RAY DIFFRACTION97.6201
2.652-2.7440.3361030.2342024X-RAY DIFFRACTION99.0685
2.744-2.8460.311970.2271969X-RAY DIFFRACTION100
2.846-2.9610.2541190.2181873X-RAY DIFFRACTION100
2.961-3.0910.248920.2221809X-RAY DIFFRACTION100
3.091-3.2390.266840.2161742X-RAY DIFFRACTION100
3.239-3.4110.221920.2081648X-RAY DIFFRACTION100
3.411-3.6140.254750.2121573X-RAY DIFFRACTION100
3.614-3.8570.218810.1971476X-RAY DIFFRACTION99.9358
3.857-4.1580.276720.1931381X-RAY DIFFRACTION100
4.158-4.5420.224770.1751247X-RAY DIFFRACTION99.9245
4.542-5.0580.177620.1621158X-RAY DIFFRACTION99.4295
5.058-5.80.151410.171036X-RAY DIFFRACTION99.446
5.8-7.010.23420.185893X-RAY DIFFRACTION99.574
7.01-9.5430.232300.195652X-RAY DIFFRACTION91.6667
9.543-200.339130.299288X-RAY DIFFRACTION63.3684

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