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- PDB-1e1t: LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH THE LY... -

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Basic information

Entry
Database: PDB / ID: 1e1t
TitleLYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH THE LYSYL_ADENYLATE INTERMEDIATE
ComponentsLYSYL-TRNA SYNTHETASE, HEAT INDUCIBLE
KeywordsLIGASE / AMINOACYL-TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS
Function / homology
Function and homology information


RNA capping / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / ligase activity / cellular response to heat / tRNA binding / magnesium ion binding / protein homodimerization activity ...RNA capping / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / ligase activity / cellular response to heat / tRNA binding / magnesium ion binding / protein homodimerization activity / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / 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 / Lysine-tRNA ligase, class II, N-terminal / 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
ADENOSINE-5'-[LYSYL-PHOSPHATE] / PYROPHOSPHATE 2- / Lysine--tRNA ligase, heat inducible / Lysine--tRNA ligase, heat inducible
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDesogus, G. / Todone, F. / Brick, P. / Onesti, S.
CitationJournal: Biochemistry / Year: 2000
Title: Active Site of Lysyl-tRNA Synthetase: Structural Studies of the Adenylation Reaction
Authors: Desogus, G. / Todone, F. / Brick, P. / Onesti, S.
History
DepositionMay 10, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2000Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary
Revision 1.2Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSYL-TRNA SYNTHETASE, HEAT INDUCIBLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,11212
Polymers57,7671
Non-polymers1,34511
Water6,071337
1
A: LYSYL-TRNA SYNTHETASE, HEAT INDUCIBLE
hetero molecules

A: LYSYL-TRNA SYNTHETASE, HEAT INDUCIBLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,22424
Polymers115,5342
Non-polymers2,68922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area15280 Å2
ΔGint-82.7 kcal/mol
Surface area35010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.100, 143.100, 176.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LYSYL-TRNA SYNTHETASE, HEAT INDUCIBLE / LYSYL-TRNA SYNTHETASE / LYSINE--TRNA LIGASE / LYSRS


Mass: 57767.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Cellular location: CYTOPLASM / Gene: LYSU / Plasmid: PXLYS5 / Gene (production host): LYSU / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG2
References: UniProt: P0A8N6, UniProt: P0A8N5*PLUS, lysine-tRNA ligase

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Non-polymers , 5 types, 348 molecules

#2: Chemical ChemComp-LAD / ADENOSINE-5'-[LYSYL-PHOSPHATE]


Mass: 475.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N7O8P
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsWHEN CRYSTALS GROWN IN THE PRESENCE OF LYSINE WERE SOAKED OVERNIGHT IN A SOLUTION CONTAINING ATP ...WHEN CRYSTALS GROWN IN THE PRESENCE OF LYSINE WERE SOAKED OVERNIGHT IN A SOLUTION CONTAINING ATP AND MG2+, THE ELECTRON DENSITY IN THE ACTIVE SITE CLEARLY SHOWED THAT THE FIRST STEP OF THE REACTION HAD OCCURRED WITHIN THE CRYSTAL WITH THE FORMATION OF THE LYSYL-ADENYLATE INTERMEDIATE. AN ADDITIONAL ELECTRON DENSITY PEAK COULD BE MODELLED AS A PARTIALLY OCCUPIED PYROPHOSPHATE MOLECULE.

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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: 4.8 Å3/Da / Density % sol: 74 %
Description: STRUCTURE WAS SOLVED BY DIFFERENCE FOURIER METHODS USING PHASES FROM 1E1O
Crystal growpH: 6.8
Details: THE PROTEIN WAS CONCENTRATED TO 12 MG/ML IN THE PRESENCE OF 5MM LYSINE AND WAS CRYSTALLISED FROM 0.1 M PIPES PH 6.8, 0.5 M LICL, 20% PEG 4K, 17% GLYCEROL; THEN, A SMALL AMOUNT OF A SOLUTION ...Details: THE PROTEIN WAS CONCENTRATED TO 12 MG/ML IN THE PRESENCE OF 5MM LYSINE AND WAS CRYSTALLISED FROM 0.1 M PIPES PH 6.8, 0.5 M LICL, 20% PEG 4K, 17% GLYCEROL; THEN, A SMALL AMOUNT OF A SOLUTION CONTAINING ATP AND MGCL2 WAS ADDED TO THE DROP TO GET A FINAL CONCENTRATION OF ABOUT 5 MM.
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
220 mMHEPES1drop
35 mMlysine1drop
42 mMbeta-mercaptoethanol1drop
520 %PEG20001reservoir
60.5 M1reservoirLiCl
70.1 MPIPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1995 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 41908 / % possible obs: 98.2 % / Redundancy: 8 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 10.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.204 / % possible all: 94.1
Reflection
*PLUS
Num. measured all: 334798
Reflection shell
*PLUS
% possible obs: 94.1 %

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E1O

1e1o


Resolution: 2.4→15 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: WHEN CRYSTALS GROWN IN THE PRESENCE OF LYSINE WERE SOAKED OVERNIGHT IN A SOLUTION CONTAINING ATP AND MG2+, THE ELECTRON DENSITY IN THE ACTIVE SITE CLEARLY SHOWED THAT THE FIRST STEP OF THE ...Details: WHEN CRYSTALS GROWN IN THE PRESENCE OF LYSINE WERE SOAKED OVERNIGHT IN A SOLUTION CONTAINING ATP AND MG2+, THE ELECTRON DENSITY IN THE ACTIVE SITE CLEARLY SHOWED THAT THE FIRST STEP OF THE REACTION HAD OCCURRED WITHIN THE CRYSTAL WITH THE FORMATION OF THE LYSYL-ADENYLATE INTERMEDIATE. AN ADDITIONAL ELECTRON DENSITY PEAK COULD BE MODELLED AS A PARTIALLY OCCUPIED PYROPHOSPHATE MOLECULE. THE ASSIGNMENT OF THE ELECTRON DENSITY PEAKS AS MG2+ IONS IS BASED ON THE POSITIONS OBSERVED FOR METAL IONS WHEN THE ELECTRON- DENSE MN2+ IONS WERE USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1639 4 %RANDOM
Rwork0.186 ---
obs0.186 40860 98 %-
Refine analyzeLuzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 85 337 4256
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d17
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.66
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.261.5
X-RAY DIFFRACTIONx_mcangle_it3.42
X-RAY DIFFRACTIONx_scbond_it4.22
X-RAY DIFFRACTIONx_scangle_it6.32.5
LS refinement shellResolution: 2.4→2.51 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.292 209 4.4 %
Rwork0.267 4675 -
obs--96.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg17
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.66

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