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- PDB-1qu3: INSIGHTS INTO EDITING FROM AN ILE-TRNA SYNTHETASE STRUCTURE WITH ... -

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Basic information

Entry
Database: PDB / ID: 1qu3
TitleINSIGHTS INTO EDITING FROM AN ILE-TRNA SYNTHETASE STRUCTURE WITH TRNA(ILE) AND MUPIROCIN
Components
  • ISOLEUCYL-TRNA
  • ISOLEUCYL-TRNA SYNTHETASE
KeywordsLIGASE/RNA / SHUTTLING MECHANISM / EDITING TRNA SYNTHETASE / DOUBLE-SIEVE / METAL IONS / HYDROLYTIC FUNCTION / LIGASE-RNA COMPLEX
Function / homology
Function and homology information


isoleucine-tRNA ligase / isoleucine-tRNA ligase activity / isoleucyl-tRNA aminoacylation / aminoacyl-tRNA deacylase activity / tRNA binding / zinc ion binding / ATP binding / cytosol
Similarity search - Function
Ile-tRNA synthetase CP2 domain-like / Class I aminoacyl-tRNA synthetases (RS) / : / Isoleucine-tRNA ligase, type 1 / Isoleucyl tRNA synthetase type 1, anticodon-binding domain / Isoleucine-tRNA ligase / hypothetical protein PF0899 fold / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Zinc finger, FPG/IleRS-type ...Ile-tRNA synthetase CP2 domain-like / Class I aminoacyl-tRNA synthetases (RS) / : / Isoleucine-tRNA ligase, type 1 / Isoleucyl tRNA synthetase type 1, anticodon-binding domain / Isoleucine-tRNA ligase / hypothetical protein PF0899 fold / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Zinc finger, FPG/IleRS-type / Zinc finger found in FPG and IleRS / Isoleucyl-tRNA Synthetase; Domain 1 / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Isoleucyl-tRNA Synthetase; Domain 1 / 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. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
MUPIROCIN / RNA / RNA (> 10) / Isoleucine--tRNA ligase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsSilvian, L.F. / Wang, J. / Steitz, T.A.
Citation
Journal: Science / Year: 1999
Title: Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin.
Authors: Silvian, L.F. / Wang, J. / Steitz, T.A.
#1: Journal: To be Published
Title: Metal Ions that Stabilize the tRNA and Mediate the Recognition by its Cognate Synthetase
Authors: Wang, J. / Silvian, L.F. / Steitz, T.A.
#2: Journal: To be Published
Title: Switching from a Resting to Synthetic and Hydrolytic Modes in Editing tRNA Synthetases
Authors: Wang, J. / Silvian, L.F. / Steitz, T.A.
#3: Journal: To be Published
Title: Structure Based Drug Design Against Mupirocin Resistant Staphylococcus Aureus
Authors: Wang, J. / Silvian, L.F. / Steitz, T.A.
History
DepositionJul 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.mon_nstd_flag / _chem_comp.pdbx_synonyms ..._chem_comp.mon_nstd_flag / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: ISOLEUCYL-TRNA
A: ISOLEUCYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8604
Polymers129,2942
Non-polymers5662
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.000, 100.000, 180.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: RNA chain ISOLEUCYL-TRNA


Mass: 24236.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein ISOLEUCYL-TRNA SYNTHETASE / E.C.6.1.1.5 / ISOLEUCINE-TRNA LIGASE / ILERS


Mass: 105057.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P41972, isoleucine-tRNA ligase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MRC / MUPIROCIN / 9-[(E)-4-[(2S,3R,4R,5S)-3,4-bis(oxidanyl)-5-[[(2S,3S)-3-[(2S,3S)-3-oxidanylbutan-2-yl]oxiran-2-yl]methyl]oxan-2-yl]-3-methyl-but-2-enoyl]oxynonanoic acid / PSEUDOMONIC ACID


Mass: 500.622 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H44O9 / Details: MUPIROCIN BUILT IN WRONG CHIRALITY
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growMethod: evaporation / Details: EVAPORATION
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.050 mMIleRS1drop
20.050 mMtRNA1drop
31 mMMupirocin1drop
412 %PEG60001reservoir
50.3 M1reservoirKCl
6100 mMsodium cacodylate1reservoir
7100 mM1reservoirMgSO4
82 mM1reservoirZnCl2
90.1 %beta-octyl glucopyranoside1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.009
DetectorType: PRINCETON 2K / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. all: 23256 / Num. obs: 23256 / % possible obs: 89.5 % / Biso Wilson estimate: 38.5 Å2 / Rsym value: 0.099
Reflection
*PLUS
Rmerge(I) obs: 0.099

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Processing

RefinementResolution: 2.9→10 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 375201.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.345 809 4.7 %RANDOM
Rwork0.234 ---
obs0.234 17042 85.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.25 Å2 / ksol: 0.312 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2---14.98 Å20 Å2
3---14.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.72 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7113 1603 36 118 8870
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.5
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d21.7
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d1.11
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it1.641.5
X-RAY DIFFRACTIONo_mcangle_it2.732
X-RAY DIFFRACTIONo_scbond_it1.942
X-RAY DIFFRACTIONo_scangle_it3.12.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.394 53 5.7 %
Rwork0.36 884 -
obs--16.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PADNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION4XPLOR_PAIRS_STUF
X-RAY DIFFRACTION5XPLOR_PA
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 4.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_angle_deg1.5
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg21.7
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg1.11
X-RAY DIFFRACTIONo_mcbond_it1.5
X-RAY DIFFRACTIONo_scbond_it2
X-RAY DIFFRACTIONo_mcangle_it2
X-RAY DIFFRACTIONo_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.394 / % reflection Rfree: 5.7 % / Rfactor Rwork: 0.36

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