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- PDB-9we9: Plasmodium vivax aspartyl-tRNA synthetase in complex with L-Asp, ... -

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Basic information

Entry
Database: PDB / ID: 9we9
TitlePlasmodium vivax aspartyl-tRNA synthetase in complex with L-Asp, Lanthanide, 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 / ASPARTIC ACID / YTTERBIUM (III) ION / aspartate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.402 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)125,79917
Polymers124,2582
Non-polymers1,54215
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint-137 kcal/mol
Surface area39390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.737, 138.737, 272.751
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, 370 molecules

#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Chemical ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Yb / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-0V1 / (2~{S})-butane-1,2,4-triol / (S)-1,2,4-butanentriol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 3.05 Å3/Da / Density % sol: 59.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Morpheous II E1: 0.1 M Buffer System 4 (MOPSO, Bis-Tris) pH 6.5, 36% Precipitant Mix 5 (30% w/v PEG 3000, 40% v/v 1, 2, 4- Butanetriol, 2% w/v NDSB 256), 2 mM Lanthanides [0.005M Yttrium(III) ...Details: Morpheous II E1: 0.1 M Buffer System 4 (MOPSO, Bis-Tris) pH 6.5, 36% Precipitant Mix 5 (30% w/v PEG 3000, 40% v/v 1, 2, 4- Butanetriol, 2% w/v NDSB 256), 2 mM Lanthanides [0.005M Yttrium(III) chloride hexahydrate, 0.005M Erbium(III) chloride hexahydrate, 0.005M Terbium(III) chloride hexahydrate, 0.005M Ytterbium(III) chloride hexahydrate]

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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 EIGER2 XE 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→128.5 Å / Num. obs: 60827 / % possible obs: 99.5 % / Redundancy: 40.4 % / CC1/2: 0.999 / Rrim(I) all: 0.09 / Net I/σ(I): 34.1
Reflection shellResolution: 2.402→2.444 Å / Mean I/σ(I) obs: 4.4 / Num. unique obs: 2986 / CC1/2: 0.935 / Rrim(I) all: 0.883 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(1.15rc1_3423: ???)refinement
autoPROCdata scaling
autoPROCdata reduction
AutoSolphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 2.402→48.628 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 3058 5.03 %
Rwork0.1753 --
obs0.1771 60801 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.402→48.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8061 0 62 355 8478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088379
X-RAY DIFFRACTIONf_angle_d0.87911313
X-RAY DIFFRACTIONf_dihedral_angle_d5.2467044
X-RAY DIFFRACTIONf_chiral_restr0.0531234
X-RAY DIFFRACTIONf_plane_restr0.0051448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4021-2.43970.28391390.20932492X-RAY DIFFRACTION97
2.4397-2.47970.24021400.19592567X-RAY DIFFRACTION99
2.4797-2.52240.25791260.18532582X-RAY DIFFRACTION100
2.5224-2.56830.25361350.18522596X-RAY DIFFRACTION100
2.5683-2.61770.20411260.1772594X-RAY DIFFRACTION100
2.6177-2.67110.22111350.18222587X-RAY DIFFRACTION100
2.6711-2.72920.23931440.18442553X-RAY DIFFRACTION99
2.7292-2.79270.21171390.18832591X-RAY DIFFRACTION100
2.7927-2.86250.2651470.19272598X-RAY DIFFRACTION100
2.8625-2.93990.27821380.19132586X-RAY DIFFRACTION100
2.9399-3.02640.26721360.19462608X-RAY DIFFRACTION100
3.0264-3.1240.20651260.18812582X-RAY DIFFRACTION99
3.124-3.23570.25791170.18672641X-RAY DIFFRACTION100
3.2357-3.36520.22881510.19832616X-RAY DIFFRACTION100
3.3652-3.51830.22891530.18132614X-RAY DIFFRACTION100
3.5183-3.70370.1951690.17672606X-RAY DIFFRACTION100
3.7037-3.93570.18881290.16172658X-RAY DIFFRACTION100
3.9357-4.23940.18441270.15452668X-RAY DIFFRACTION100
4.2394-4.66570.1741450.13722652X-RAY DIFFRACTION99
4.6657-5.34020.17771390.15172714X-RAY DIFFRACTION100
5.3402-6.72520.21231530.19272734X-RAY DIFFRACTION100
6.7252-48.6280.20331440.18942904X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 18.9099 Å / Origin y: 54.8321 Å / Origin z: 14.1388 Å
111213212223313233
T0.3716 Å20.0438 Å20.096 Å2-0.3019 Å20.0107 Å2--0.3138 Å2
L0.8945 °20.2481 °2-0.1103 °2-1.0094 °20.0611 °2--0.5784 °2
S-0.0219 Å °-0.0535 Å °0.0892 Å °0.1644 Å °0.0449 Å °0.0579 Å °-0.0564 Å °0.0366 Å °-0.0113 Å °
Refinement TLS groupSelection details: all

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