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- PDB-9we8: Plasmodium vivax aspartyl-tRNA synthetase (PvDRS) complexed with ... -

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Basic information

Entry
Database: PDB / ID: 9we8
TitlePlasmodium vivax aspartyl-tRNA synthetase (PvDRS) complexed with the non-hydrolysable ATP analogue AMP-PCP (ACP)
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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / HEXANE-1,6-DIOL / aspartate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.395 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)125,89910
Polymers124,2582
Non-polymers1,6418
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11370 Å2
ΔGint-38 kcal/mol
Surface area40940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.940, 140.940, 275.880
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-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: 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
#4: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Morpheus D3: 0.1 M Buffer System 1 (Imidazole and MES monohydrate (acid)) pH 6.5, Precipitant Mix 3 (40% v/v Glycerol and 20% w/v PEG 4000), and 0.12 M Alcohols (0.2 M 1,6-Hexanediol; 0.2 M ...Details: Morpheus D3: 0.1 M Buffer System 1 (Imidazole and MES monohydrate (acid)) pH 6.5, Precipitant Mix 3 (40% v/v Glycerol and 20% w/v PEG 4000), and 0.12 M Alcohols (0.2 M 1,6-Hexanediol; 0.2 M 1-Butanol 0.2 M 1,2-Propanediol; 0.2M 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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.395→141.04 Å / Num. obs: 64240 / % possible obs: 99.8 % / Redundancy: 40.6 % / CC1/2: 0.99 / Rrim(I) all: 0.206 / Net I/σ(I): 17.2
Reflection shellResolution: 2.395→2.54 Å / Mean I/σ(I) obs: 0.98 / Num. unique obs: 10187 / CC1/2: 0.565 / Rrim(I) all: 2.694 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.15rc1_3423-000)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9M5M

9m5m


Resolution: 2.395→46.133 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 3206 5 %
Rwork0.1812 --
obs0.1828 64151 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.395→46.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8114 0 104 464 8682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038456
X-RAY DIFFRACTIONf_angle_d0.6511424
X-RAY DIFFRACTIONf_dihedral_angle_d3.47090
X-RAY DIFFRACTIONf_chiral_restr0.0461243
X-RAY DIFFRACTIONf_plane_restr0.0041485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.395-2.43080.39041320.3122502X-RAY DIFFRACTION96
2.4308-2.46880.26631370.282600X-RAY DIFFRACTION100
2.4688-2.50920.29151350.26862597X-RAY DIFFRACTION100
2.5092-2.55250.30921370.272597X-RAY DIFFRACTION100
2.5525-2.59890.30961380.27282611X-RAY DIFFRACTION100
2.5989-2.64890.30911380.30022637X-RAY DIFFRACTION100
2.6489-2.7030.32641370.27522597X-RAY DIFFRACTION100
2.703-2.76170.26031390.25282632X-RAY DIFFRACTION100
2.7617-2.8260.32751360.22752593X-RAY DIFFRACTION100
2.826-2.89660.25431380.20812620X-RAY DIFFRACTION100
2.8966-2.97490.25881390.20852639X-RAY DIFFRACTION100
2.9749-3.06250.26311390.20752640X-RAY DIFFRACTION100
3.0625-3.16130.25521380.20672616X-RAY DIFFRACTION100
3.1613-3.27420.20921390.2062636X-RAY DIFFRACTION100
3.2742-3.40530.24081390.19092641X-RAY DIFFRACTION100
3.4053-3.56020.21681390.17792649X-RAY DIFFRACTION100
3.5602-3.74780.21141400.16322662X-RAY DIFFRACTION100
3.7478-3.98250.17791400.15072668X-RAY DIFFRACTION100
3.9825-4.28980.15951420.142688X-RAY DIFFRACTION100
4.2898-4.72110.13821420.12742698X-RAY DIFFRACTION100
4.7211-5.40340.18121430.14642722X-RAY DIFFRACTION100
5.4034-6.80420.2291450.1832759X-RAY DIFFRACTION100
6.8042-46.1330.20051540.18832941X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 17.9231 Å / Origin y: 55.4138 Å / Origin z: 13.8882 Å
111213212223313233
T0.3116 Å20.0274 Å20.0472 Å2-0.4013 Å20.0074 Å2--0.3296 Å2
L1.0513 °2-0.0159 °2-0.1674 °2-1.0727 °20.251 °2--0.8417 °2
S0.0173 Å °-0.0801 Å °0.0746 Å °0.0976 Å °-0.0022 Å °-0.0075 Å °-0.0496 Å °0.0815 Å °-0.0097 Å °
Refinement TLS groupSelection details: all

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