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- PDB-9wee: Plasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMP... -

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Basic information

Entry
Database: PDB / ID: 9wee
TitlePlasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMP 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
ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE / aspartate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsSharma, V.K. / Manickam, Y. / 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)125,6519
Polymers124,2582
Non-polymers1,3937
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-72 kcal/mol
Surface area39240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.986, 139.986, 274.052
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 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
#2: Chemical ChemComp-AMO / ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE


Mass: 462.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19N6O10P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ProPlex C4: 0.1 M Sodium citrate pH 6.0, 20% w/v PEG 4000, 0.2 M Lithium 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: Apr 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.32→121.231 Å / Num. obs: 69192 / % possible obs: 100 % / Redundancy: 39.7 % / CC1/2: 0.999 / Rrim(I) all: 0.256 / Net I/σ(I): 15.9
Reflection shellResolution: 2.32→2.36 Å / Redundancy: 29.7 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3410 / CC1/2: 0.355 / % 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
Starting model: 9M5M

9m5m


Resolution: 2.32→121.231 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2173 3502 5.07 %
Rwork0.19 --
obs0.1913 69126 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→121.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8053 0 90 378 8521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048351
X-RAY DIFFRACTIONf_angle_d0.69511288
X-RAY DIFFRACTIONf_dihedral_angle_d2.8196996
X-RAY DIFFRACTIONf_chiral_restr0.051236
X-RAY DIFFRACTIONf_plane_restr0.0041472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3204-2.35220.37711470.31262526X-RAY DIFFRACTION99
2.3522-2.38580.32811360.29352586X-RAY DIFFRACTION100
2.3858-2.42140.31891340.27932601X-RAY DIFFRACTION100
2.4214-2.45930.25221230.27012580X-RAY DIFFRACTION100
2.4593-2.49960.2841480.27332588X-RAY DIFFRACTION100
2.4996-2.54270.28031290.26162577X-RAY DIFFRACTION100
2.5427-2.58890.25071330.24712598X-RAY DIFFRACTION100
2.5889-2.63870.29751240.24452587X-RAY DIFFRACTION100
2.6387-2.69260.25921430.23512597X-RAY DIFFRACTION100
2.6926-2.75110.25481350.22062589X-RAY DIFFRACTION100
2.7511-2.81510.22661320.21892593X-RAY DIFFRACTION100
2.8151-2.88560.21081390.2092602X-RAY DIFFRACTION100
2.8856-2.96360.22841350.22462603X-RAY DIFFRACTION100
2.9636-3.05080.29061590.22112597X-RAY DIFFRACTION100
3.0508-3.14930.22251430.21322579X-RAY DIFFRACTION100
3.1493-3.26180.23091520.20032625X-RAY DIFFRACTION100
3.2618-3.39240.21511340.19372622X-RAY DIFFRACTION100
3.3924-3.54680.20051460.18082618X-RAY DIFFRACTION100
3.5468-3.73390.21381540.16872615X-RAY DIFFRACTION100
3.7339-3.96780.19581360.1612651X-RAY DIFFRACTION100
3.9678-4.27420.18611460.15052657X-RAY DIFFRACTION100
4.2742-4.70430.15721420.13622672X-RAY DIFFRACTION100
4.7043-5.3850.17681400.15422716X-RAY DIFFRACTION100
5.385-6.78450.22241480.19312726X-RAY DIFFRACTION100
6.7845-121.2310.21681440.19642919X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 17.9275 Å / Origin y: 55.1084 Å / Origin z: 13.8499 Å
111213212223313233
T0.293 Å20.0212 Å20.055 Å2-0.4013 Å2-0.0035 Å2--0.3169 Å2
L0.8906 °20.0978 °2-0.1529 °2-1.1154 °20.127 °2--0.7927 °2
S0.0452 Å °-0.1208 Å °0.0538 Å °0.0972 Å °-0.0205 Å °-0.0068 Å °-0.088 Å °0.0807 Å °-0.0222 Å °
Refinement TLS groupSelection details: all

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