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- PDB-9wea: Plasmodium vivax aspartyl-tRNA synthetase in complex with AMP, PO... -

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Basic information

Entry
Database: PDB / ID: 9wea
TitlePlasmodium vivax aspartyl-tRNA synthetase in complex with AMP, PO4, MOPS and Alcohols
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
ADENOSINE MONOPHOSPHATE / HEXANE-1,6-DIOL / 1,3-PROPANDIOL / S-1,2-PROPANEDIOL / PHOSPHATE ION / aspartate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 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)126,54922
Polymers124,2582
Non-polymers2,29220
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13520 Å2
ΔGint-96 kcal/mol
Surface area39720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.470, 138.470, 273.050
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 , 8 types, 332 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#7: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Morpheus-D8: 0.1 M Buffer System 2 (Sodium HEPES; MOPS) pH 7.5, 37.5% Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350) and 0.12 M Alcohols (0.2 M 1,6-Hexanediol; 0.2 M 1- ...Details: Morpheus-D8: 0.1 M Buffer System 2 (Sodium HEPES; MOPS) pH 7.5, 37.5% Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350) and 0.12 M Alcohols (0.2 M 1,6-Hexanediol; 0.2 M 1-Butanol 0.2 M 1,2-Propanediol; 0.2 M 2-Propanol; 0.2 M 1,4-Butanediol; 0.2 M 1,3- Propanediol)

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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 EIGER2 XE 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: 2.301→119.919 Å / Num. obs: 128148 / % possible obs: 99.7 % / Redundancy: 39.6 % / CC1/2: 0.999 / Rrim(I) all: 0.173 / Net I/σ(I): 18.1
Reflection shellResolution: 2.301→2.341 Å / Redundancy: 28.7 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3256 / CC1/2: 0.345 / % possible all: 96.2

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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: 2.301→50.071 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 6471 5.05 %
Rwork0.1849 --
obs0.1866 128148 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.301→50.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8054 0 138 312 8504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038408
X-RAY DIFFRACTIONf_angle_d0.64911371
X-RAY DIFFRACTIONf_dihedral_angle_d2.8526974
X-RAY DIFFRACTIONf_chiral_restr0.0441241
X-RAY DIFFRACTIONf_plane_restr0.0031448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3012-2.32740.34471940.33133114X-RAY DIFFRACTION77
2.3274-2.35470.34251820.31993595X-RAY DIFFRACTION86
2.3547-2.38340.34032010.30914032X-RAY DIFFRACTION98
2.3834-2.41360.30561960.28294081X-RAY DIFFRACTION99
2.4136-2.44540.28061950.28644121X-RAY DIFFRACTION100
2.4454-2.47890.3392560.27994089X-RAY DIFFRACTION100
2.4789-2.51430.332110.26994091X-RAY DIFFRACTION100
2.5143-2.55180.27312050.2624167X-RAY DIFFRACTION100
2.5518-2.59170.28192140.25234055X-RAY DIFFRACTION100
2.5917-2.63420.32972160.25814149X-RAY DIFFRACTION100
2.6342-2.67960.28112210.23834079X-RAY DIFFRACTION100
2.6796-2.72830.282090.22844144X-RAY DIFFRACTION100
2.7283-2.78080.27792150.2264116X-RAY DIFFRACTION100
2.7808-2.83750.26812330.21954114X-RAY DIFFRACTION100
2.8375-2.89920.22992000.20954105X-RAY DIFFRACTION100
2.8992-2.96670.26582100.20714118X-RAY DIFFRACTION100
2.9667-3.04090.24482660.20644054X-RAY DIFFRACTION100
3.0409-3.12310.24032200.20314116X-RAY DIFFRACTION100
3.1231-3.21490.24792300.19994143X-RAY DIFFRACTION100
3.2149-3.31870.23742110.24065X-RAY DIFFRACTION100
3.3187-3.43730.21732320.17964109X-RAY DIFFRACTION100
3.4373-3.57490.21872560.18054087X-RAY DIFFRACTION100
3.5749-3.73750.24352080.17334149X-RAY DIFFRACTION100
3.7375-3.93450.19692010.16044111X-RAY DIFFRACTION100
3.9345-4.18090.18772340.14874091X-RAY DIFFRACTION100
4.1809-4.50350.13862040.13564126X-RAY DIFFRACTION100
4.5035-4.95630.1982160.13884117X-RAY DIFFRACTION100
4.9563-5.67270.1892210.16394099X-RAY DIFFRACTION100
5.6727-7.14370.20722160.19534119X-RAY DIFFRACTION100
7.1437-50.0710.18911980.17524121X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 18.6172 Å / Origin y: 54.3626 Å / Origin z: 13.7713 Å
111213212223313233
T0.3967 Å20.0766 Å20.0981 Å2-0.4025 Å20.0208 Å2--0.3458 Å2
L1.0216 °20.1784 °2-0.1095 °2-1.2196 °20.1592 °2--0.6705 °2
S-0.046 Å °-0.0672 Å °0.0945 Å °0.1605 Å °0.0875 Å °0.0398 Å °-0.045 Å °0.0323 Å °-0.0292 Å °
Refinement TLS groupSelection details: all

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