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- PDB-1ile: ISOLEUCYL-TRNA SYNTHETASE -

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Basic information

Entry
Database: PDB / ID: 1ile
TitleISOLEUCYL-TRNA SYNTHETASE
ComponentsISOLEUCYL-TRNA SYNTHETASE
KeywordsAMINOACYL-TRNA SYNTHETASE / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


isoleucine-tRNA ligase / isoleucine-tRNA ligase activity / isoleucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Domain of unknown function (DUF5915) / Isoleucine-tRNA ligase, type 2 / Isoleucyl tRNA synthetase type 2, anticodon-binding domain / Isoleucine-tRNA ligase / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) ...Domain of unknown function (DUF5915) / Isoleucine-tRNA ligase, type 2 / Isoleucyl tRNA synthetase type 2, anticodon-binding domain / Isoleucine-tRNA ligase / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / 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. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Isoleucine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsNureki, O. / Vassylyev, D.G. / Tateno, M. / Shimada, A. / Nakama, T. / Fukai, S. / Konno, M. / Schimmel, P. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Science / Year: 1998
Title: Enzyme structure with two catalytic sites for double-sieve selection of substrate.
Authors: Nureki, O. / Vassylyev, D.G. / Tateno, M. / Shimada, A. / Nakama, T. / Fukai, S. / Konno, M. / Hendrickson, T.L. / Schimmel, P. / Yokoyama, S.
History
DepositionFeb 24, 1998Processing site: BNL
Revision 1.0Apr 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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
A: ISOLEUCYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8133
Polymers94,6821
Non-polymers1312
Water5,801322
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.100, 94.800, 126.500
Angle α, β, γ (deg.)90.00, 126.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ISOLEUCYL-TRNA SYNTHETASE / ILERS


Mass: 94682.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PK7 / Production host: Escherichia coli (E. coli) / References: UniProt: P56690
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 30

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Sample preparation

CrystalDensity Matthews: 4.11 Å3/Da / Density % sol: 63 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
212 %PEG40001reservoir
36 %isopropanol1reservoir
41 %MPD1reservoir
560 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 48290 / % possible obs: 91 % / Observed criterion σ(I): 0.1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.064 / Rsym value: 0.102 / Net I/σ(I): 8.14
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.5 % / % possible all: 76.3
Reflection
*PLUS
Num. measured all: 134577
Reflection shell
*PLUS
% possible obs: 76.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→15 Å / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.298 -10 %RANDOM
Rwork0.222 ---
obs0.222 46804 --
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6698 0 2 322 7022
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.25
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.65
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.65

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