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- PDB-1e24: LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM complexed with lysine... -

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Entry
Database: PDB / ID: 1e24
TitleLYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM complexed with lysine and ATP and MN2+
ComponentsLYSYL-TRNA SYNTHETASE
KeywordsLIGASE / AMINOACYL-TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS
Function / homologyLysine-tRNA ligase, class II / Aminoacyl-tRNA synthetase, class II (D/K/N) / Aminoacyl-transfer RNA synthetases class-II family profile. / OB-fold nucleic acid binding domain / tRNA synthetases class II (D, K and N) / Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Nucleic acid-binding, OB-fold / Aminoacyl-tRNA synthetase, class II / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type ...Lysine-tRNA ligase, class II / Aminoacyl-tRNA synthetase, class II (D/K/N) / Aminoacyl-transfer RNA synthetases class-II family profile. / OB-fold nucleic acid binding domain / tRNA synthetases class II (D, K and N) / Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Nucleic acid-binding, OB-fold / Aminoacyl-tRNA synthetase, class II / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / ligase activity / nucleic acid binding / magnesium ion binding / membrane / ATP binding / cytosol / cytoplasm / Lysine--tRNA ligase, heat inducible / Lysine--tRNA ligase, heat inducible
Function and homology information
Specimen sourceESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / 2.35 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 16, 2000 / Release: Jul 28, 2000
RevisionDateData content typeGroupProviderType
1.0Jul 28, 2000Structure modelrepositoryInitial release
1.1Aug 24, 2011Structure modelAtomic model / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7718
Polyers57,7671
Non-polymers1,0037
Water6,485360
1
A: LYSYL-TRNA SYNTHETASE
hetero molecules

A: LYSYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,54116
Polyers115,5342
Non-polymers2,00714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area (Å2)12480
ΔGint (kcal/M)-78.4
Surface area (Å2)36440
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)143.600, 143.600, 177.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP 61 2 2

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide LYSYL-TRNA SYNTHETASE


Mass: 57767.191 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Cellular location: CYTOPLASM / Gene: LYSU / Plasmid name: PXLYS5 / Gene (production host): LYSU / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG2
References: UniProt: P14825, UniProt: P0A8N5*PLUS, lysine-tRNA ligase

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Non-polymers , 5 types, 367 molecules

#2: Chemical ChemComp-LYS / LYSINE


Mass: 147.195 Da / Num. of mol.: 1 / Formula: C6H15N2O2 / Lysine
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Formula: Mn / Manganese
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Formula: C3H8O3 / Glycerol
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Formula: H2O / Water

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Details

Compound detailsWHEN CRYSTALS GROWN IN THE PRESENCE OF LYSINE WERE SOAKED IN A SOLUTION CONTAINING ATP AND MNCL2 ...WHEN CRYSTALS GROWN IN THE PRESENCE OF LYSINE WERE SOAKED IN A SOLUTION CONTAINING ATP AND MNCL2 FOR AN HOUR, THE FIRST STEP OF THE REACTION DOES NOT OCCUR AND THE RESULTING MODEL SHOWS THE CONFORMATION OF THE ATP SUBSTRATE BEFORE THE REACTION.

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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 / Density percent sol: 74 %
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 CONTAINING ATP AND MNCL2 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
IDConcCommon 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: 1 kelvins
SourceSource: SYNCHROTRON / Type: SRS BEAMLINE PX9.6 / Synchrotron site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Details: MIRROR / Detector: IMAGE PLATE / Collection date: Sep 15, 1998
RadiationMonochromator: SI(111) / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionD resolution high: 2.35 Å / D resolution low: 65 Å / Number obs: 45104 / Rmerge I obs: 0.072 / Rsym value: 0.072 / NetI over sigmaI: 15.5 / Redundancy: 4.9 % / Percent possible obs: 99.4
Reflection shellRmerge I obs: 0.182 / Highest resolution: 2.35 Å / Lowest resolution: 2.48 Å / MeanI over sigI obs: 7.3 / Rsym value: 0.182 / Redundancy: 4.2 % / Percent possible all: 99
Reflection
*PLUS
Number measured all: 217414
Reflection shell
*PLUS
Percent possible obs: 99

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefineMethod to determine structure: OTHER
Details: THREE WELL DEFINED ELECTRON DENSITY PEAKS WERE OBSERVED ANDINTERPRETED AS MN2+ IONS. ONE IS COORDINATED BY THE ALPHA AND BETA PHOSPHATE AND TWO CARBOXYLATE (GLU 414 AND GLU 421) AND THE OTHER TWO BRIDGE THE BETA AND GAMMA PHOSPHATES.
R Free selection details: RANDOM / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Least-squares processR factor R free: 0.249 / R factor R free error: 0.006 / R factor R work: .182 / R factor obs: .182 / Highest resolution: 2.35 Å / Lowest resolution: 25 Å / Number reflection R free: 1834 / Number reflection obs: 45066 / Percent reflection R free: 4 / Percent reflection obs: 99.4
Refine analyzeLuzzati d res low obs: 25 Å
Refine hist #LASTHighest resolution: 2.35 Å / Lowest resolution: 25 Å
Number of atoms included #LASTProtein: 3871 / Nucleic acid: 0 / Ligand: 56 / Solvent: 360 / Total: 4287
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.391.5
X-RAY DIFFRACTIONx_mcangle_it3.662.0
X-RAY DIFFRACTIONx_scbond_it4.522.0
X-RAY DIFFRACTIONx_scangle_it6.92.5
Refine LS shellHighest resolution: 2.35 Å / R factor R free: 0.248 / R factor R free error: 0.017 / R factor R work: 0.249 / Lowest resolution: 2.46 Å / Number reflection R free: 215 / Number reflection R work: 5213 / Total number of bins used: 8 / Percent reflection R free: 4 / Percent reflection obs: 98.7
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO
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_deg22.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.1

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