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- PDB-9weg: Plasmodium vivax aspartyl-tRNA synthetase in complex with AMS, Mg... -

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Basic information

Entry
Database: PDB / ID: 9weg
TitlePlasmodium vivax aspartyl-tRNA synthetase in complex with AMS, Mg ion, Iodides and Pentaethylene glycol
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
IODIDE ION / Chem-LMS / aspartate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.228 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

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)125,93912
Polymers124,2582
Non-polymers1,68210
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11380 Å2
ΔGint-55 kcal/mol
Surface area39580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.685, 138.685, 274.992
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-

IOD

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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, 385 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-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Morpheus B5: 0.1 M Buffer System 2 pH 7.5 (Sodium HEPES and MOPS), 30% Precipitant Mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000) and 0.09 M Halogens (0.3 M Sodium fluoride; 0.3 M Sodium ...Details: Morpheus B5: 0.1 M Buffer System 2 pH 7.5 (Sodium HEPES and MOPS), 30% Precipitant Mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000) and 0.09 M Halogens (0.3 M Sodium fluoride; 0.3 M Sodium bromide; 0.3 M Sodium iodide)

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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: 2.228→120.105 Å / Num. obs: 76798 / % possible obs: 100 % / Redundancy: 37.6 % / CC1/2: 0.997 / Rrim(I) all: 0.196 / Net I/σ(I): 16.2
Reflection shellResolution: 2.228→2.267 Å / Redundancy: 20.9 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3784 / CC1/2: 0.261 / % 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: 2.228→45.832 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2208 3854 5.05 %
Rwork0.1895 --
obs0.1911 76368 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.228→45.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8132 0 74 375 8581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048497
X-RAY DIFFRACTIONf_angle_d0.70411486
X-RAY DIFFRACTIONf_dihedral_angle_d5.5627176
X-RAY DIFFRACTIONf_chiral_restr0.0471247
X-RAY DIFFRACTIONf_plane_restr0.0041499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2282-2.25540.35411410.3382287X-RAY DIFFRACTION90
2.2554-2.2840.33571130.3322508X-RAY DIFFRACTION97
2.284-2.3140.33691330.3252525X-RAY DIFFRACTION98
2.314-2.34570.32941340.29322531X-RAY DIFFRACTION100
2.3457-2.37920.29661270.28112570X-RAY DIFFRACTION100
2.3792-2.41470.2741310.25492548X-RAY DIFFRACTION100
2.4147-2.45250.25631450.24882560X-RAY DIFFRACTION100
2.4525-2.49270.30541510.24352554X-RAY DIFFRACTION100
2.4927-2.53560.28191300.24232575X-RAY DIFFRACTION100
2.5356-2.58170.31541430.24342555X-RAY DIFFRACTION100
2.5817-2.63140.27291130.23052586X-RAY DIFFRACTION100
2.6314-2.68510.2811460.21822562X-RAY DIFFRACTION100
2.6851-2.74350.22341310.20392584X-RAY DIFFRACTION100
2.7435-2.80730.26031080.20112604X-RAY DIFFRACTION100
2.8073-2.87750.2111310.20032600X-RAY DIFFRACTION100
2.8775-2.95530.22851320.20022597X-RAY DIFFRACTION100
2.9553-3.04220.26211470.21652564X-RAY DIFFRACTION100
3.0422-3.14040.25211520.20952579X-RAY DIFFRACTION100
3.1404-3.25260.21841400.21142597X-RAY DIFFRACTION100
3.2526-3.38280.24051510.1942605X-RAY DIFFRACTION100
3.3828-3.53670.18481430.19132601X-RAY DIFFRACTION100
3.5367-3.72310.23361220.17762626X-RAY DIFFRACTION100
3.7231-3.95620.19341440.15832635X-RAY DIFFRACTION100
3.9562-4.26150.1841310.1472631X-RAY DIFFRACTION100
4.2615-4.68990.13811390.13362668X-RAY DIFFRACTION100
4.6899-5.36770.18241530.14982669X-RAY DIFFRACTION100
5.3677-6.75930.23271500.19722717X-RAY DIFFRACTION100
6.7593-45.8320.22931730.19212876X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.1619 Å / Origin y: 54.5191 Å / Origin z: 14.1348 Å
111213212223313233
T0.3414 Å20.0476 Å20.0759 Å2-0.3584 Å20.0271 Å2--0.3346 Å2
L0.7933 °20.1363 °20 °2-1.0892 °20.1368 °2--0.6395 °2
S-0.0115 Å °-0.0294 Å °0.0947 Å °0.0955 Å °0.034 Å °0.0172 Å °-0.0638 Å °0.0109 Å °-0.0149 Å °
Refinement TLS groupSelection details: all

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