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- PDB-1lyl: LYSYL-TRNA SYNTHETASE (LYSU) (E.C.6.1.1.6) COMPLEXED WITH LYSINE -

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Basic information

Entry
Database: PDB / ID: 1lyl
TitleLYSYL-TRNA SYNTHETASE (LYSU) (E.C.6.1.1.6) COMPLEXED WITH LYSINE
ComponentsLYSYL-TRNA SYNTHETASE (LYSU)
KeywordsLIGASE (SYNTHETASE)
Function / homology
Function and homology information


RNA capping / ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / tRNA aminoacylation for protein translation / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / ligase activity ...RNA capping / ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / tRNA aminoacylation for protein translation / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / ligase activity / cellular response to heat / tRNA binding / magnesium ion binding / protein homodimerization activity / extracellular space / ATP binding / membrane / cytosol
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
LYSINE / Lysine--tRNA ligase, heat inducible
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsOnesti, S. / Brick, P.
Citation
Journal: Structure / Year: 1995
Title: The crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia coli
Authors: Onesti, S. / Miller, A.D. / Brick, P.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary Diffraction Studies of E.Coli Lysyl-T(Slash)RNA Synthetase (Lysu)
Authors: Onesti, S. / Theoclitou, M.-E. / Wittung, E.P.L. / Miller, A.D. / Plateau, P. / Blanquet, S. / Brick, P.
History
DepositionMay 3, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: LYSYL-TRNA SYNTHETASE (LYSU)
B: LYSYL-TRNA SYNTHETASE (LYSU)
C: LYSYL-TRNA SYNTHETASE (LYSU)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,7436
Polymers173,3023
Non-polymers4423
Water6,756375
1
A: LYSYL-TRNA SYNTHETASE (LYSU)
C: LYSYL-TRNA SYNTHETASE (LYSU)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,8294
Polymers115,5342
Non-polymers2942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-39 kcal/mol
Surface area37250 Å2
MethodPISA
2
B: LYSYL-TRNA SYNTHETASE (LYSU)
hetero molecules

B: LYSYL-TRNA SYNTHETASE (LYSU)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,8294
Polymers115,5342
Non-polymers2942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)144.270, 257.800, 182.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsSYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: B 14 .. 504 CRYSTALLOGRAPHIC DYAD OPERATION SYMMETRY1 1 1.000000 0.000000 0.000000 0.00000 SYMMETRY2 1 0.000000 -1.000000 0.000000 257.80000 SYMMETRY3 1 0.000000 0.000000 -1.000000 182.08000 APPLIED TO RESIDUES: Y 1 .. 1 CRYSTALLOGRAPHIC DYAD OPERATION SYMMETRY1 2 1.000000 0.000000 0.000000 0.00000 SYMMETRY2 2 0.000000 -1.000000 0.000000 257.80000 SYMMETRY3 2 0.000000 0.000000 -1.000000 182.08000 THE ASYMMETRIC UNIT CAN ALSO BE DESCRIBED AS CONTAINING THREE SUBUNITS ARRANGED AROUND A PSEUDO 31 AXIS PARALLEL TO THE CRYSTALLOGRAPHIC C AXIS, RELATING SUBUNITS *B*, *A* AND *C'* WHERE *C'* IS CRYSTALLOGRAPHICALLY RELATED TO SUBUNIT *C*.

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Components

#1: Protein LYSYL-TRNA SYNTHETASE (LYSU)


Mass: 57767.191 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A8N5, lysine-tRNA ligase
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.88 Å3/Da / Density % sol: 74.81 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
250 mMHEPES1drop
32 mMbeta-mercaptoethanol1drop
45 mMlysine1drop
50.1 MPIPES1reservoir
620 %(w/v)PEG20001reservoir
70.5 M1reservoirLiCl

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Data collection

DetectorDate: Aug 25, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→12 Å / Num. obs: 76222 / % possible obs: 92.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 %
Reflection
*PLUS
Rmerge(I) obs: 0.078

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Processing

Software
NameVersionClassification
MOSFLM/CCP4data collection
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data reduction
X-PLOR3.1phasing
RefinementResolution: 2.8→12 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.238 -4 %
Rwork0.193 --
obs0.193 73174 92.8 %
Displacement parametersBiso mean: 24.75 Å2
Refinement stepCycle: LAST / Resolution: 2.8→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11376 0 0 375 11751
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.32
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_d
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

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