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- PDB-9wec: Plasmodium vivax aspartyl-tRNA synthetase in complex with AMP, Di... -

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Basic information

Entry
Database: PDB / ID: 9wec
TitlePlasmodium vivax aspartyl-tRNA synthetase in complex with AMP, Divalent metals, 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-6BY / ADENOSINE MONOPHOSPHATE / : / : / aspartate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.391 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

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)126,27222
Polymers124,2582
Non-polymers2,01520
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11460 Å2
ΔGint-235 kcal/mol
Surface area39880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.032, 139.032, 273.339
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-705-

CL

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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, 294 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#6: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-6BY / (2R)-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
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 59.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Morpheus II-B1: 0.1 M Buffer System 4 pH 6.5 (MOPSO, Bis-Tris), 35% Precipitant Mix 5 (0% w/v PEG 3000, 40% v/v 1, 2, 4- Butanetriol, 2% w/v NDSB 256) 2 mM Divalents II (0.005 M Manganese(II) ...Details: Morpheus II-B1: 0.1 M Buffer System 4 pH 6.5 (MOPSO, Bis-Tris), 35% Precipitant Mix 5 (0% w/v PEG 3000, 40% v/v 1, 2, 4- Butanetriol, 2% w/v NDSB 256) 2 mM Divalents II (0.005 M Manganese(II) chloride tetrahydrate, 0.005 M Cobalt(II) chloride hexahydrate , 0.005 M Nickel(II) chloride hexahydrate, 0.005 M Zinc acetate dihydrate)

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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: 2.391→120.405 Å / Num. obs: 62198 / % possible obs: 99.8 % / Redundancy: 40.7 % / CC1/2: 0.999 / Rrim(I) all: 0.262 / Net I/σ(I): 13.2
Reflection shellResolution: 2.391→2.432 Å / Redundancy: 38.8 % / Num. unique obs: 3002 / CC1/2: 0.413 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.15rc1_3423: ???)refinement
autoPROCdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9M5M

9m5m


Resolution: 2.391→110.188 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 3049 4.96 %
Rwork0.192 --
obs0.1936 61528 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.391→110.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8097 0 101 274 8472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058411
X-RAY DIFFRACTIONf_angle_d0.7811364
X-RAY DIFFRACTIONf_dihedral_angle_d5.2387026
X-RAY DIFFRACTIONf_chiral_restr0.0481238
X-RAY DIFFRACTIONf_plane_restr0.0051450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3912-2.42860.36631200.36082249X-RAY DIFFRACTION85
2.4286-2.46840.37211460.3522426X-RAY DIFFRACTION93
2.4684-2.5110.39411380.33872538X-RAY DIFFRACTION96
2.511-2.55660.37231330.3242626X-RAY DIFFRACTION99
2.5566-2.60580.36681420.28762610X-RAY DIFFRACTION100
2.6058-2.6590.32961280.25752664X-RAY DIFFRACTION100
2.659-2.71680.26991280.24112652X-RAY DIFFRACTION100
2.7168-2.780.30941430.21712656X-RAY DIFFRACTION100
2.78-2.84950.25741430.22682640X-RAY DIFFRACTION100
2.8495-2.92660.27981400.21982644X-RAY DIFFRACTION100
2.9266-3.01270.23491360.21532676X-RAY DIFFRACTION100
3.0127-3.110.27251280.21522668X-RAY DIFFRACTION100
3.11-3.22110.24291320.21362682X-RAY DIFFRACTION100
3.2211-3.35010.24711350.20262676X-RAY DIFFRACTION100
3.3501-3.50260.24161560.18812685X-RAY DIFFRACTION100
3.5026-3.68730.21851430.18032687X-RAY DIFFRACTION100
3.6873-3.91830.21671470.16522693X-RAY DIFFRACTION100
3.9183-4.22080.16361260.16242729X-RAY DIFFRACTION100
4.2208-4.64560.15471290.13522755X-RAY DIFFRACTION100
4.6456-5.31780.20741620.15462728X-RAY DIFFRACTION100
5.3178-6.69980.23161480.19872800X-RAY DIFFRACTION100
6.6998-110.1880.20221460.20062995X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.5914 Å / Origin y: 54.8857 Å / Origin z: 13.9892 Å
111213212223313233
T0.4148 Å20.0676 Å20.0948 Å2-0.3942 Å20.0278 Å2--0.3768 Å2
L0.9947 °20.1438 °2-0.1291 °2-1.219 °20.1481 °2--0.6821 °2
S-0.0569 Å °-0.0572 Å °0.086 Å °0.1595 Å °0.0859 Å °0.028 Å °-0.0532 Å °0.0348 Å °-0.0206 Å °
Refinement TLS groupSelection details: all

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