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- PDB-1bbu: LYSYL-TRNA SYNTHETASE (LYSS) COMPLEXED WITH LYSINE -

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Basic information

Entry
Database: PDB / ID: 1bbu
TitleLYSYL-TRNA SYNTHETASE (LYSS) COMPLEXED WITH LYSINE
ComponentsPROTEIN (LYSYL-TRNA SYNTHETASE)
KeywordsLIGASE / AMINOACYL-TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / ligase activity / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsOnesti, S. / Desogus, G. / Brevet, A. / Chen, J. / Plateau, P. / Blanquet, S. / Brick, P.
Citation
Journal: Biochemistry / Year: 2000
Title: Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding.
Authors: Onesti, S. / Desogus, G. / Brevet, A. / Chen, J. / Plateau, P. / Blanquet, S. / Brick, P.
#1: Journal: Structure / Year: 1995
Title: Crystal Structure of the Lysyl-tRNA Synthetase (Lysu) from Escherichia Coli
Authors: Onesti, S. / Miller, A.D. / Brick, P.
#2: Journal: J.Biol.Chem. / Year: 1995
Title: Comparison of the Enzymatic Properties of Two Escherichia Coli Lysyl-tRNA Synthetase Species
Authors: Brevet, A. / Chen, J. / Leveque, F. / Blanquet, S. / Plateau, P.
History
DepositionApr 24, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: PROTEIN (LYSYL-TRNA SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6932
Polymers57,5461
Non-polymers1471
Water2,720151
1
A: PROTEIN (LYSYL-TRNA SYNTHETASE)
hetero molecules

A: PROTEIN (LYSYL-TRNA SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,3874
Polymers115,0922
Non-polymers2942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area8430 Å2
ΔGint-32 kcal/mol
Surface area38260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)181.820, 181.820, 93.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein PROTEIN (LYSYL-TRNA SYNTHETASE)


Mass: 57546.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cellular location: CYTOPLASMICCytoplasm / Gene: LYSS / Plasmid: PXLYSKS1 / Production host: Escherichia coli (E. coli) / Strain (production host): PAL2103UKTR / References: UniProt: P0A8N3, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 3.86 Å3/Da / Density % sol: 68 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Density % sol: 68 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220 mMTris-HCl1drop
310 mM2-mercaptoethanol1drop
410 mM1dropMgCl2
50.1 MHEPES1reservoir
646-50 %satammonium sulfate1reservoir
72-4 %PEG4001reservoir
815-20 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1999 / Details: MIRROR
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 25113 / % possible obs: 99.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.071 / Rsym value: 7.1 / Net I/σ(I): 6
Reflection shellResolution: 2.7→2.84 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 3.2 / Rsym value: 22.2 / % possible all: 99.1
Reflection
*PLUS
Num. measured all: 87419
Reflection shell
*PLUS
% possible obs: 99.1 %

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LYL

1lyl


Resolution: 2.7→20 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRENTION APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1206 5 %RANDOM
Rwork0.228 ---
obs0.228 24986 98.7 %-
Displacement parametersBiso mean: 55 Å2
Refine analyzeLuzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3789 0 10 151 3950
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.44
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.187
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it5.351.5
X-RAY DIFFRACTIONx_mcangle_it7.832
X-RAY DIFFRACTIONx_scbond_it5.882
X-RAY DIFFRACTIONx_scangle_it8.522.5
LS refinement shellResolution: 2.7→2.82 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.48 134 5 %
Rwork0.43 2919 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 55 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.187
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Rfactor Rfree: 0.48 / % reflection Rfree: 5 % / Rfactor Rwork: 0.43

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