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- PDB-9weh: Plasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMS... -

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Basic information

Entry
Database: PDB / ID: 9weh
TitlePlasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMS, SO4, MOPSO and Butanetriol
Componentsaspartate--tRNA ligase
KeywordsLIGASE / AMINOACYLATION / AMINOACYL-TRNA SYNTHETASE / TRNA-BINDING / ATP-BINDING / MALARIA / INHIBITOR
Function / homology
Function and homology information


aspartate-tRNA ligase / aspartate-tRNA ligase activity / aspartyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / RNA binding / ATP binding / cytosol
Similarity search - Function
Aspartate-tRNA synthetase, type 2 / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / 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
(2~{S})-butane-1,2,4-triol / Chem-6BX / 5'-O-(L-alpha-aspartylsulfamoyl)adenosine / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / aspartate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.094 Å
AuthorsManickam, Y. / Sharma, V.K. / Bagale, S. / Pradeepkumar, P.I. / Sharma, A.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)PR32713 India
Indian Council of Medical ResearchCAR grant 2024-000140 India
CitationJournal: To Be Published
Title: The active site of aspartyl-tRNA synthetase: Structural studies of the adenylation reaction and flexibility of residues.
Authors: Sharma, V.K. / Manickam, Y. / Sharma, A.
History
DepositionAug 19, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 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: aspartate--tRNA ligase
B: aspartate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,74318
Polymers124,2582
Non-polymers2,48516
Water12,827712
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10230 Å2
ΔGint-85 kcal/mol
Surface area39400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.779, 139.779, 274.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-703-

SO4

21A-1180-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein aspartate--tRNA ligase / Aspartyl-tRNA synthetase


Mass: 62128.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVC01_020016700, PVW1_020019400 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1G4H6Y1, aspartate-tRNA ligase

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Non-polymers , 8 types, 728 molecules

#2: Chemical ChemComp-DSZ / 5'-O-(L-alpha-aspartylsulfamoyl)adenosine


Mass: 461.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19N7O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-0V1 / (2~{S})-butane-1,2,4-triol / (S)-1,2,4-butanentriol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-6BX / (2S)-2-hydroxy-3-(morpholin-4-yl)propane-1-sulfonic acid


Mass: 225.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO5S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Morpheus II-A1: Butanetriol 0.1 M Buffer System 4 pH 6.5 (MOPSO, Bis-Tris), 36% Precipitant Mix 5 (30% w/v PEG 3000, 40% v/v 1, 2, 4- Butanetriol, 2% w/v NDSB 256) and 90 mM LiNaK (0.3 M ...Details: Morpheus II-A1: Butanetriol 0.1 M Buffer System 4 pH 6.5 (MOPSO, Bis-Tris), 36% Precipitant Mix 5 (30% w/v PEG 3000, 40% v/v 1, 2, 4- Butanetriol, 2% w/v NDSB 256) and 90 mM LiNaK (0.3 M Lithium sulfate, 0.3 M Sodium sulfate, 0.3 M Potassium sulfate)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.094→121.052 Å / Num. obs: 93328 / % possible obs: 100 % / Redundancy: 40.8 % / CC1/2: 0.999 / Rrim(I) all: 0.294 / Net I/σ(I): 13.3
Reflection shellResolution: 2.094→2.13 Å / Redundancy: 42.2 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4558 / CC1/2: 0.315 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.15rc1_3423: ???)refinement
autoPROCdata scaling
autoPROCdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.094→50.459 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2106 4583 4.95 %
Rwork0.1751 --
obs0.1769 92673 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.094→50.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8078 0 160 712 8950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048479
X-RAY DIFFRACTIONf_angle_d0.73911450
X-RAY DIFFRACTIONf_dihedral_angle_d5.3627075
X-RAY DIFFRACTIONf_chiral_restr0.0471239
X-RAY DIFFRACTIONf_plane_restr0.0041491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.094-2.11770.32351260.31322507X-RAY DIFFRACTION86
2.1177-2.14260.32791500.31112752X-RAY DIFFRACTION95
2.1426-2.16880.34191370.29022871X-RAY DIFFRACTION99
2.1688-2.19620.30091430.27572891X-RAY DIFFRACTION99
2.1962-2.22510.31131450.2652934X-RAY DIFFRACTION100
2.2251-2.25560.30271380.25732936X-RAY DIFFRACTION100
2.2556-2.28780.29311350.24832911X-RAY DIFFRACTION100
2.2878-2.3220.26691710.2422892X-RAY DIFFRACTION100
2.322-2.35830.28321580.23782908X-RAY DIFFRACTION100
2.3583-2.39690.25381640.23262911X-RAY DIFFRACTION100
2.3969-2.43820.28411410.22452913X-RAY DIFFRACTION100
2.4382-2.48260.28151550.22482938X-RAY DIFFRACTION100
2.4826-2.53030.26251460.2172924X-RAY DIFFRACTION100
2.5303-2.5820.23781740.20452899X-RAY DIFFRACTION100
2.582-2.63810.23921480.19582949X-RAY DIFFRACTION100
2.6381-2.69950.23951280.192959X-RAY DIFFRACTION100
2.6995-2.7670.21031580.18192914X-RAY DIFFRACTION100
2.767-2.84180.22941900.17162911X-RAY DIFFRACTION100
2.8418-2.92540.18361560.17332946X-RAY DIFFRACTION100
2.9254-3.01980.2111560.17452932X-RAY DIFFRACTION100
3.0198-3.12770.20911690.1672941X-RAY DIFFRACTION100
3.1277-3.25290.21231690.16312945X-RAY DIFFRACTION100
3.2529-3.4010.20971590.16342965X-RAY DIFFRACTION100
3.401-3.58020.19281570.15532975X-RAY DIFFRACTION100
3.5802-3.80450.18251350.14513005X-RAY DIFFRACTION100
3.8045-4.09810.16141390.14033026X-RAY DIFFRACTION100
4.0981-4.51030.14031910.12192981X-RAY DIFFRACTION100
4.5103-5.16230.17731430.13553055X-RAY DIFFRACTION100
5.1623-6.50180.20411470.17743095X-RAY DIFFRACTION100
6.5018-50.4590.25241550.19653304X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 17.7795 Å / Origin y: 54.6432 Å / Origin z: 13.571 Å
111213212223313233
T0.2396 Å20.015 Å20.0513 Å2-0.3187 Å2-0.0113 Å2--0.2327 Å2
L1.0848 °20.1966 °2-0.2089 °2-1.0417 °2-0.0273 °2--0.6862 °2
S0.0456 Å °-0.1499 Å °0.0661 Å °0.1384 Å °-0.0216 Å °0.0263 Å °-0.0853 Å °0.0937 Å °-0.0138 Å °
Refinement TLS groupSelection details: all

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