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- PDB-9wef: Plasmodium vivax aspartyl-tRNA synthetase in complex with AMS and SO4 -

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Basic information

Entry
Database: PDB / ID: 9wef
TitlePlasmodium vivax aspartyl-tRNA synthetase in complex with AMS and SO4
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
Chem-LMS / aspartate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsManickam, Y. / Sharma, V.K. / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)125,73612
Polymers124,2582
Non-polymers1,47810
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11470 Å2
ΔGint-113 kcal/mol
Surface area39610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.698, 139.698, 272.186
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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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 , 6 types, 299 molecules

#2: Chemical ChemComp-LMS / [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE


Type: RNA linking / Mass: 346.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N6O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 3.09 Å3/Da / Density % sol: 60.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: SG1-E12: 0.1 M Sodium HEPES pH 7.5, 25% w/v PEG 3350 and 0.2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97627 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 2.402→120.982 Å / Num. obs: 61783 / % possible obs: 100 % / Redundancy: 40.4 % / CC1/2: 0.999 / Rrim(I) all: 0.119 / Net I/σ(I): 28.9
Reflection shellResolution: 2.402→2.444 Å / Redundancy: 35.7 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3009 / CC1/2: 0.796 / % possible all: 99.3

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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: 2.402→110.553 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2188 3097 5.01 %
Rwork0.1808 --
obs0.1827 61766 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.402→110.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7990 0 85 289 8364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068268
X-RAY DIFFRACTIONf_angle_d0.79911187
X-RAY DIFFRACTIONf_dihedral_angle_d5.2466889
X-RAY DIFFRACTIONf_chiral_restr0.051224
X-RAY DIFFRACTIONf_plane_restr0.0051460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4021-2.43960.33051460.2652558X-RAY DIFFRACTION99
2.4396-2.47960.25981490.23392608X-RAY DIFFRACTION100
2.4796-2.52240.27221420.23332620X-RAY DIFFRACTION100
2.5224-2.56830.29691380.21812641X-RAY DIFFRACTION100
2.5683-2.61770.23081360.20042601X-RAY DIFFRACTION100
2.6177-2.67110.23811520.19452613X-RAY DIFFRACTION100
2.6711-2.72920.26231260.18992636X-RAY DIFFRACTION100
2.7292-2.79270.21991440.18792644X-RAY DIFFRACTION100
2.7927-2.86250.23881370.19272634X-RAY DIFFRACTION100
2.8625-2.93990.23331270.19822633X-RAY DIFFRACTION100
2.9399-3.02650.21561380.20982651X-RAY DIFFRACTION100
3.0265-3.12410.2371480.20882640X-RAY DIFFRACTION100
3.1241-3.23580.25841520.19032623X-RAY DIFFRACTION100
3.2358-3.36540.23161180.19422688X-RAY DIFFRACTION100
3.3654-3.51850.23471190.1872687X-RAY DIFFRACTION100
3.5185-3.70410.2171240.1862681X-RAY DIFFRACTION100
3.7041-3.93610.19731410.16922668X-RAY DIFFRACTION100
3.9361-4.24010.19991360.15252717X-RAY DIFFRACTION100
4.2401-4.66680.1661430.13272712X-RAY DIFFRACTION100
4.6668-5.3420.17531610.15272705X-RAY DIFFRACTION100
5.342-6.73030.26051510.19562771X-RAY DIFFRACTION100
6.7303-110.5530.21681690.19212938X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.7818 Å / Origin y: 55.0031 Å / Origin z: 13.9742 Å
111213212223313233
T0.334 Å20.036 Å20.089 Å2-0.3579 Å2-0.0004 Å2--0.3105 Å2
L0.8242 °20.2892 °2-0.0885 °2-1.2329 °20.011 °2--0.7022 °2
S0.0629 Å °-0.0781 Å °0.1063 Å °0.1922 Å °-0.0015 Å °0.0609 Å °-0.0992 Å °0.035 Å °-0.033 Å °
Refinement TLS groupSelection details: all

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