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- PDB-8z1p: Crystal structure of Saccharomyces cerevisiae isoleucyl-tRNA synt... -

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Basic information

Entry
Database: PDB / ID: 8z1p
TitleCrystal structure of Saccharomyces cerevisiae isoleucyl-tRNA synthetase in complex with a mimic tRNA(Met) and isoleucine
Components
  • isoleucine--tRNA ligase
  • tRNA(Met)
KeywordsLIGASE/RNA / LIGASE-RNA COMPLEX
Function / homology(2S,3S)-2-amino-3-methylpentane-1,1-diol / RNA / RNA (> 10) / :
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 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
DepositionApr 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 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.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: isoleucine--tRNA ligase
B: tRNA(Met)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,8223
Polymers148,6892
Non-polymers1331
Water1267
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)52.662, 81.206, 106.171
Angle α, β, γ (deg.)78.39, 83.65, 71.78
Int Tables number1
Space group name H-MP1

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Components

#1: Protein isoleucine--tRNA ligase


Mass: 124213.367 Da / Num. of mol.: 1
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(Met)


Mass: 24475.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Chemical ChemComp-IL0 / (2S,3S)-2-amino-3-methylpentane-1,1-diol


Type: peptide-like / Mass: 133.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 2% TacsimateTM pH 6.0, 0.1 M BIS-TRIS pH 6.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.83→75.92 Å / Num. obs: 36523 / % possible obs: 93.9 % / Redundancy: 1.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.049 / Rrim(I) all: 0.069 / Χ2: 0.94 / Net I/σ(I): 10 / Num. measured all: 65750
Reflection shellResolution: 2.83→2.99 Å / % possible obs: 96 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.239 / Num. measured all: 9698 / Num. unique obs: 5453 / CC1/2: 0.926 / Rpim(I) all: 0.239 / Rrim(I) all: 0.338 / Χ2: 0.76 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→75.92 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.863 / SU B: 19.459 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R Free: 0.492 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27772 1393 4.7 %RANDOM
Rwork0.23662 ---
obs0.23848 28351 76.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.865 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å22.27 Å2-3.72 Å2
2---4.46 Å22.6 Å2
3---4.83 Å2
Refinement stepCycle: 1 / Resolution: 2.83→75.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7608 1365 9 7 8989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0129333
X-RAY DIFFRACTIONr_bond_other_d0.0020.0187044
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.60113083
X-RAY DIFFRACTIONr_angle_other_deg1.4061.6716150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.48251056
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94623.075335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.93315933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7651525
X-RAY DIFFRACTIONr_chiral_restr0.0510.21363
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022119
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_it4.1097.6444239
X-RAY DIFFRACTIONr_mcbond_other4.1097.6454238
X-RAY DIFFRACTIONr_mcangle_it6.35411.4755290
X-RAY DIFFRACTIONr_mcangle_other6.35411.4745291
X-RAY DIFFRACTIONr_scbond_it4.0387.9535094
X-RAY DIFFRACTIONr_scbond_other4.0377.9535095
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.08711.9637794
X-RAY DIFFRACTIONr_long_range_B_refined8.21687.96410132
X-RAY DIFFRACTIONr_long_range_B_other8.21587.96210133
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.832→2.906 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 84 -
Rwork0.355 2192 -
obs--77.44 %

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