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- PDB-9kwd: Crystal structure of E.coli LysU complexing with LysSA and ATP -

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Basic information

Entry
Database: PDB / ID: 9kwd
TitleCrystal structure of E.coli LysU complexing with LysSA and ATP
ComponentsLysine--tRNA ligase, heat inducible
KeywordsLIGASE / Complex / Aminoacyl-tRNA synthetase
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 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. ...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 / 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, OB-fold
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / DI(HYDROXYETHYL)ETHER / Lysine--tRNA ligase, heat inducible
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsXia, M. / Hei, Z. / Fang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of E.coli LysU complexing with LysSA and ATP
Authors: Xia, M. / Hei, Z. / Fang, P.
History
DepositionDec 5, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysine--tRNA ligase, heat inducible
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1757
Polymers57,7691
Non-polymers1,4066
Water18010
1
A: Lysine--tRNA ligase, heat inducible
hetero molecules

A: Lysine--tRNA ligase, heat inducible
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,35114
Polymers115,5382
Non-polymers2,81212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area8140 Å2
ΔGint-40 kcal/mol
Surface area38190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.849, 146.849, 182.025
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 Lysine--tRNA ligase, heat inducible / Lysyl-tRNA synthetase / LysRS


Mass: 57769.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lysU, b4129, JW4090 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A8N5, lysine-tRNA ligase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-KAA / 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / 5'-O-[N-(L-LYSYL)SULFAMOYL]ADENOSINE


Mass: 474.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N8O7S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.9 Å3/Da / Density % sol: 74.92 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: Magnesium chloride, Sodium acetate, PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97855 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 33187 / % possible obs: 86.4 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 17.09
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.411 / Num. unique obs: 3256 / % possible all: 67.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.49→48.07 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2539 657 5.09 %
Rwork0.2243 --
obs0.2259 12917 84.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.49→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3951 0 0 10 3961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114042
X-RAY DIFFRACTIONf_angle_d1.3525467
X-RAY DIFFRACTIONf_dihedral_angle_d10.184564
X-RAY DIFFRACTIONf_chiral_restr0.065599
X-RAY DIFFRACTIONf_plane_restr0.019711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.49-3.760.6314710.60361517X-RAY DIFFRACTION53
3.76-4.140.26981080.29342000X-RAY DIFFRACTION71
4.14-4.740.14851420.13132815X-RAY DIFFRACTION98
4.74-5.970.19251470.15862885X-RAY DIFFRACTION100
5.97-48.070.22781890.19343043X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 64.3879 Å / Origin y: 1.2493 Å / Origin z: 11.9703 Å
111213212223313233
T0.335 Å20.0388 Å2-0.0349 Å2-0.2954 Å20.0171 Å2--0.4851 Å2
L0.2174 °20.3285 °2-0.1619 °2-1.6517 °2-0.167 °2--0.4937 °2
S0.0518 Å °-0.0697 Å °-0.0026 Å °0.1194 Å °0.077 Å °0.073 Å °0.0456 Å °-0.0845 Å °-0.095 Å °
Refinement TLS groupSelection details: all

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