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- PDB-8wnd: Crystal structure of Saccharomyces cerevisiae isoleucyl-tRNA synt... -

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Basic information

Entry
Database: PDB / ID: 8wnd
TitleCrystal structure of Saccharomyces cerevisiae isoleucyl-tRNA synthetase in complex with tRNA(Ile) and isoleucine
Components
  • isoleucine--tRNA ligase
  • tRNA(Ile)
KeywordsLIGASE/RNA / LIGASELIGASE-RNA complex / LIGASE-RNA complex
Function / homologyISOLEUCINE / RNA / RNA (> 10) / :
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChen, B. / Yi, F. / Zhou, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22207133 China
National Natural Science Foundation of China (NSFC)22177140 China
CitationJournal: Nat Commun / Year: 2024
Title: The mechanism of discriminative aminoacylation by isoleucyl-tRNA synthetase based on wobble nucleotide recognition.
Authors: Chen, B. / Yi, F. / Luo, Z. / Lu, F. / Liu, H. / Luo, S. / Gu, Q. / Zhou, H.
History
DepositionOct 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 22, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: isoleucine--tRNA ligase
T: tRNA(Ile)
B: isoleucine--tRNA ligase
R: tRNA(Ile)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,35716
Polymers298,1684
Non-polymers1,18912
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.428, 173.521, 171.803
Angle α, β, γ (deg.)90.00, 91.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / RNA chain , 2 types, 4 molecules ABTR

#1: Protein isoleucine--tRNA ligase


Mass: 124213.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ILS1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5Q0L4
#2: RNA chain tRNA(Ile)


Mass: 24870.770 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 4 types, 220 molecules

#3: Chemical ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M BIS-TRIS pH5.5, 25% PEG3350, 0.06 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.8→48.73 Å / Num. obs: 75496 / % possible obs: 98.3 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.049 / Rrim(I) all: 0.091 / Χ2: 1.02 / Net I/σ(I): 12.1
Reflection shellResolution: 2.8→2.86 Å / % possible obs: 99.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.607 / Num. measured all: 15467 / Num. unique obs: 4447 / CC1/2: 0.771 / Rpim(I) all: 0.379 / Rrim(I) all: 0.718 / Χ2: 0.97 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48.73 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.899 / SU B: 18.031 / SU ML: 0.348 / Cross valid method: THROUGHOUT / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26793 3604 4.8 %RANDOM
Rwork0.22991 ---
obs0.23171 71849 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.812 Å2
Baniso -1Baniso -2Baniso -3
1-3.92 Å2-0 Å2-3.05 Å2
2---1.06 Å20 Å2
3----2.74 Å2
Refinement stepCycle: 1 / Resolution: 2.8→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15068 3102 67 208 18445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01218954
X-RAY DIFFRACTIONr_bond_other_d0.0020.01814972
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.59926528
X-RAY DIFFRACTIONr_angle_other_deg1.2951.67834467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57351982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78422.62729
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.061152217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1911571
X-RAY DIFFRACTIONr_chiral_restr0.0520.22691
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219546
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024272
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_it2.76.5927979
X-RAY DIFFRACTIONr_mcbond_other2.76.5927978
X-RAY DIFFRACTIONr_mcangle_it4.3299.8819944
X-RAY DIFFRACTIONr_mcangle_other4.3299.8819945
X-RAY DIFFRACTIONr_scbond_it2.7017.3610975
X-RAY DIFFRACTIONr_scbond_other2.687.36210940
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.28411.09616531
X-RAY DIFFRACTIONr_long_range_B_refined6.28876.76920730
X-RAY DIFFRACTIONr_long_range_B_other6.28476.78220711
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 326 -
Rwork0.344 5248 -
obs--99.15 %

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