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- PDB-36lw: Crystal structure of a Lysine--tRNA ligase (LysRS) from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 36lw
TitleCrystal structure of a Lysine--tRNA ligase (LysRS) from Pseudomonas aeruginosa
ComponentsLysine--tRNA ligase
KeywordsRIBOSOMAL PROTEIN / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Lysine--tRNA ligase / Pseudomonas aeruginosa
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / protein homodimerization activity / ATP binding / cytoplasm / cytosol
Similarity search - Function
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
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: To be published
Title: Crystal structure of a Lysine--tRNA ligase (LysRS) from Pseudomonas aeruginosa
Authors: Lanyi Lari, N. / Ung, A.R. / Lovell, S. / Cooper, A. / Battaile, K.P.
History
DepositionJun 17, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,58315
Polymers114,8402
Non-polymers74313
Water17,943996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11550 Å2
ΔGint-120 kcal/mol
Surface area39640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.886, 96.064, 88.001
Angle α, β, γ (deg.)90.00, 105.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lysine--tRNA ligase / Lysyl-tRNA synthetase / LysRS


Mass: 57419.953 Da / Num. of mol.: 2 / Fragment: H9-Q500
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: lysS, PA3700 / Plasmid: PsaeA.00612.a.B3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HXU0, lysine-tRNA ligase

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Non-polymers , 5 types, 1009 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 996 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris, pH 8.5, 200 mM NaCl, 25% PEG 3350, PsaeA.00612.a.B3.PW39509 at 15 mg/mL. 12A_25-112 drop C12, Puck: PSL-0115, Cryo: 20% PEG200 + 80% crystallant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: May 26, 2026
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.62→48.03 Å / Num. obs: 118369 / % possible obs: 97.5 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.037 / Rrim(I) all: 0.098 / Χ2: 1.01 / Net I/σ(I): 11.6 / Num. measured all: 834515
Reflection shellResolution: 1.62→1.65 Å / % possible obs: 96.1 % / Redundancy: 7.3 % / Rmerge(I) obs: 1.278 / Num. measured all: 42182 / Num. unique obs: 5746 / CC1/2: 0.679 / Rpim(I) all: 0.504 / Rrim(I) all: 1.375 / Χ2: 1.03 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIXdev_6082refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→48.03 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1909 5733 4.85 %
Rwork0.1637 --
obs0.1651 118320 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7659 0 39 996 8694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058026
X-RAY DIFFRACTIONf_angle_d0.74810880
X-RAY DIFFRACTIONf_dihedral_angle_d16.923108
X-RAY DIFFRACTIONf_chiral_restr0.0471195
X-RAY DIFFRACTIONf_plane_restr0.011438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.640.32571720.26873672X-RAY DIFFRACTION96
1.64-1.660.25871830.24713709X-RAY DIFFRACTION96
1.66-1.680.26691890.23833669X-RAY DIFFRACTION96
1.68-1.70.26951960.23213677X-RAY DIFFRACTION96
1.7-1.720.24961860.22823725X-RAY DIFFRACTION96
1.72-1.750.26371960.21963686X-RAY DIFFRACTION97
1.75-1.770.2551800.21643726X-RAY DIFFRACTION96
1.77-1.80.24242120.21383684X-RAY DIFFRACTION96
1.8-1.820.25111960.21413719X-RAY DIFFRACTION97
1.82-1.850.26361570.21533740X-RAY DIFFRACTION97
1.85-1.890.2251510.20213803X-RAY DIFFRACTION97
1.89-1.920.24191720.19933720X-RAY DIFFRACTION97
1.92-1.960.23571800.18013734X-RAY DIFFRACTION97
1.96-20.21561910.16633739X-RAY DIFFRACTION97
2-2.040.20012070.16863710X-RAY DIFFRACTION97
2.04-2.090.17631860.1633761X-RAY DIFFRACTION97
2.09-2.140.18411790.16273796X-RAY DIFFRACTION98
2.14-2.20.19221660.15813730X-RAY DIFFRACTION98
2.2-2.260.19741900.15213782X-RAY DIFFRACTION98
2.26-2.340.20091930.15213752X-RAY DIFFRACTION98
2.34-2.420.17772040.15293797X-RAY DIFFRACTION98
2.42-2.520.19611810.1533794X-RAY DIFFRACTION98
2.52-2.630.19522030.15443763X-RAY DIFFRACTION99
2.63-2.770.17892150.16113788X-RAY DIFFRACTION98
2.77-2.940.20292260.16463757X-RAY DIFFRACTION98
2.94-3.170.21292140.16573808X-RAY DIFFRACTION99
3.17-3.490.1961780.15253828X-RAY DIFFRACTION98
3.49-3.990.14582100.13453805X-RAY DIFFRACTION98
3.99-5.030.13742300.12233811X-RAY DIFFRACTION99
5.03-48.030.18411900.18273902X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9235-0.1210.24862.9860.06760.97740.0028-0.12280.04520.08970.0317-0.1356-0.05960.0784-0.04970.1237-0.009-0.00320.210.01380.121217.3132.742451.9998
20.9282-0.3670.86990.5187-0.43771.25070.09850.0508-0.1061-0.018-0.0613-0.00480.12280.156-0.05780.15180.01610.01970.19560.0070.1619-1.4191-1.54419.3588
31.26660.12450.49870.18470.05160.89010.02340.2112-0.1429-0.09440.00160.00440.07370.2306-0.02230.16030.03150.00880.1724-0.00760.15042.57575.37530.6001
41.7849-0.6182-0.112.00120.55831.80940.08490.03980.0917-0.1332-0.04060.0895-0.0992-0.1064-0.03840.14820.0076-00.09860.02120.1284-30.04719.21340.9116
51.1581-1.2461.4391.5872-0.94934.69110.0242-0.1535-0.2301-0.01260.11010.19680.3268-0.5534-0.14650.1884-0.0472-0.02760.21860.02240.2219-30.35370.769.9195
61.8053-0.31420.71030.6536-0.02360.9480.1128-0.0025-0.1554-0.0559-0.0395-0.01230.10610.0263-0.07270.1505-0.00960.0140.17350.04760.1572-6.995-4.509629.256
71.16680.2292-0.21821.7066-0.81641.35940.0548-0.0177-0.07940.0702-0.03540.0360.04260.0319-0.01980.13650.00670.00360.15880.00390.134-21.9334-6.692249.8783
80.831-0.24550.29040.1462-0.28320.84290.0514-0.1025-0.1799-0.0230.03880.04610.0895-0.0519-0.18060.1609-0.014-0.01120.17830.03190.2003-8.9108-9.45739.7151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 143 )
2X-RAY DIFFRACTION2chain 'A' and (resid 144 through 282 )
3X-RAY DIFFRACTION3chain 'A' and (resid 283 through 499 )
4X-RAY DIFFRACTION4chain 'B' and (resid 11 through 143 )
5X-RAY DIFFRACTION5chain 'B' and (resid 144 through 173 )
6X-RAY DIFFRACTION6chain 'B' and (resid 174 through 282 )
7X-RAY DIFFRACTION7chain 'B' and (resid 283 through 393 )
8X-RAY DIFFRACTION8chain 'B' and (resid 394 through 499 )

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