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- PDB-1e1o: lysyl-tRNA Synthetase (LYSU) hexagonal form, complexed with lysine -

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Basic information

Entry
Database: PDB / ID: 1e1o
Titlelysyl-tRNA Synthetase (LYSU) hexagonal form, complexed with lysine
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
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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 9, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2000Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Mar 29, 2017Group: Derived calculations / Structure summary
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_site
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_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, HEAT INDUCIBLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,65110
Polymers57,7671
Non-polymers8849
Water6,503361
1
A: LYSYL-TRNA SYNTHETASE, HEAT INDUCIBLE
hetero molecules

A: LYSYL-TRNA SYNTHETASE, HEAT INDUCIBLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,30220
Polymers115,5342
Non-polymers1,76818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area12750 Å2
ΔGint-42.5 kcal/mol
Surface area36560 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
DetailsTHE PROTEIN IS AN ACTIVE DIMER. IN THE HEXAGONAL CELL THEMOLECULAR DYADE COINCIDE WITH A CRYSTALLOGRAPHIC 2-FOLDAXIS. TO GENERATE THE BIOLOGICALLY FUNCTIONAL DIMER THESYMMETRY OPERATION Y , X, -Z+1/3 NEEDS TO BE APPLIED TO THEATOMIC COORDINATES.

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Components

#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: P0A8N5, lysine-tRNA ligase
#2: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE STRUCTURE OF E. COLI LYSYL-TRNA SYNTHETASE LYSU BOUND TO THE SUBSTRATE LYSINE HAS BEEN SOLVED ...THE STRUCTURE OF E. COLI LYSYL-TRNA SYNTHETASE LYSU BOUND TO THE SUBSTRATE LYSINE HAS BEEN SOLVED AT LOWER (2.8 A) RESOLUTION (PDB ID 1LYL) FROM AN ORTHORHOMBIC SPACE GROUP CONTAINING 3 MONOMERS IN THE ASYMMETRIC UNIT ARRANGED AROUND A PSEUDO 31 AXIS. CRYSTALS OF LYSU:LYSINE COMPLEX OBTAINED IN THE PRESENCE OF GLYCEROL AND USED FOR THE HIGH RESOLUTION STRUCTURE DISPLAY A SIMILAR HABIT TO THE ORIGINAL ORTHORHOMBIC CRYSTALS BUT BELONG TO A RELATED HEXAGONAL CRYSTAL FORM. IN SPITE OF THE DRAMATIC CHANGE IN SPACE GROUP THERE IS ONLY A MINOR REARRANGEMENT OF THE CRYSTAL LATTICE AND THE HEXAGONAL CRYSTAL FORM COULD BE SOLVED BY USING THE 1LYL MODEL TRANSLATED TO ACCOUNT FOR THE DIFFERENT ORIGIN OF THE HEXAGONAL CELL.

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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 USING 1LYL COORDINATED TRANSLATED TO ACCOUNT FOR THE DIFFERENT ORIGIN OF THE RELATED HEXAGONAL CELL
Crystal growpH: 6.8
Details: PROTEIN WAS CRYSTALLISED FROM 0.1M PIPES PH 6.8, 0.5 M LICL; 20% PEG 4K, 17% GLYCEROL
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: BW7B / Wavelength: 0.86
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: 0.86 Å / Relative weight: 1
ReflectionResolution: 2.12→25 Å / Num. obs: 60434 / % possible obs: 99.6 % / Redundancy: 16.2 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 8.8
Reflection shellResolution: 2.12→2.16 Å / Redundancy: 15.4 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.26 / % possible all: 99.6
Reflection
*PLUS
Num. measured all: 977338
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

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

1lyl


Resolution: 2.12→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2301 4 %RANDOM
Rwork0.195 ---
obs0.195 57124 99.6 %-
Refine analyzeLuzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.12→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3815 0 58 361 4234
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_d23.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.17
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.132
X-RAY DIFFRACTIONx_mcangle_it3.362.5
X-RAY DIFFRACTIONx_scbond_it4.112.5
X-RAY DIFFRACTIONx_scangle_it6.413
LS refinement shellResolution: 2.12→2.22 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.301 202 4.2 %
Rwork0.262 4728 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.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_deg23.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.17

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