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- PDB-6ldk: Isoleucyl-tRNA synthetase from Candida albicans complexed with a ... -

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Basic information

Entry
Database: PDB / ID: 6ldk
TitleIsoleucyl-tRNA synthetase from Candida albicans complexed with a isoleucyl-adenylate
ComponentsIsoleucine--tRNA ligase
KeywordsTRANSLATION / tRNA synthetase
Function / homology
Function and homology information


isoleucine-tRNA ligase / isoleucine-tRNA ligase activity / isoleucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / ATP binding / cytosol
Similarity search - Function
Domain of unknown function (DUF5915) / Isoleucine-tRNA ligase, type 2 / Isoleucyl tRNA synthetase type 2, anticodon-binding domain / Isoleucine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding ...Domain of unknown function (DUF5915) / Isoleucine-tRNA ligase, type 2 / Isoleucyl tRNA synthetase type 2, anticodon-binding domain / Isoleucine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / 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
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / ISOLEUCINE / isoleucine--tRNA ligase
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsCho, Y. / Chung, S.
CitationJournal: Mol.Cells / Year: 2020
Title: Structural Basis for the Antibiotic Resistance of Eukaryotic Isoleucyl-tRNA Synthetase.
Authors: Chung, S. / Kim, S. / Ryu, S.H. / Hwang, K.Y. / Cho, Y.
History
DepositionNov 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoleucine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,8303
Polymers99,3511
Non-polymers4782
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-2 kcal/mol
Surface area33330 Å2
Unit cell
Length a, b, c (Å)56.491, 137.618, 73.752
Angle α, β, γ (deg.)90.000, 106.307, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Isoleucine--tRNA ligase / isoleucyl-tRNA synthetase


Mass: 99351.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Strain: SC5314 / Gene: ILS1, orf19.2138, CAALFM_C604520WA / Production host: Escherichia coli (E. coli) / References: UniProt: Q59RI1, isoleucine-tRNA ligase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: MES, PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→49.4 Å / Num. obs: 23469 / % possible obs: 98.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 58.5 Å2 / CC1/2: 0.989 / Net I/σ(I): 11.5
Reflection shellResolution: 2.9→2.95 Å / Num. unique obs: 23469 / CC1/2: 0.459

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ILE

1ile


Resolution: 2.9→49.34 Å / SU ML: 0.3387 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.6254 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2394 1164 5 %
Rwork0.1725 22139 -
obs0.1759 23303 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.46 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6666 0 31 4 6701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00956881
X-RAY DIFFRACTIONf_angle_d1.06619339
X-RAY DIFFRACTIONf_chiral_restr0.0537997
X-RAY DIFFRACTIONf_plane_restr0.0081185
X-RAY DIFFRACTIONf_dihedral_angle_d9.61014132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.31341390.2382664X-RAY DIFFRACTION93.93
3.03-3.190.32791490.22352820X-RAY DIFFRACTION99.23
3.19-3.390.30041470.21032788X-RAY DIFFRACTION98.32
3.39-3.650.26731450.1932782X-RAY DIFFRACTION98.45
3.65-4.020.23831430.17132721X-RAY DIFFRACTION94.87
4.02-4.60.25571440.14882748X-RAY DIFFRACTION96.85
4.6-5.80.19531500.1522834X-RAY DIFFRACTION99.3
5.8-49.320.18341470.15222782X-RAY DIFFRACTION96.32

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