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- PDB-9wem: Plasmodium vivax aspartyl-tRNA synthetase in combination with Asp... -

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Basic information

Entry
Database: PDB / ID: 9wem
TitlePlasmodium vivax aspartyl-tRNA synthetase in combination with Asp-AMS, Mg ion, MOPS and PGE
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
5'-O-(L-alpha-aspartylsulfamoyl)adenosine / TRIETHYLENE GLYCOL / aspartate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.128 Å
AuthorsManickam, Y. / Sharma, V.K. / Bagale, S. / Pradeepkumar, P.I. / 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)125,98011
Polymers124,3722
Non-polymers1,6099
Water10,593588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10350 Å2
ΔGint-50 kcal/mol
Surface area40230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.008, 139.008, 273.343
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-1034-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein aspartate--tRNA ligase / Aspartyl-tRNA synthetase


Mass: 62185.859 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 , 7 types, 597 molecules

#2: Chemical ChemComp-DSZ / 5'-O-(L-alpha-aspartylsulfamoyl)adenosine


Mass: 461.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19N7O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / 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: 3.06 Å3/Da / Density % sol: 59.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Morepheus F5: 0.1 M Buffer System 2 pH 7.5 (Sodium HEPES and MOPS), 30% Precipitant Mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000) and 0.12 M Monosaccharides (0.2 M D-Glucose; 0.2 M D- ...Details: Morepheus F5: 0.1 M Buffer System 2 pH 7.5 (Sodium HEPES and MOPS), 30% Precipitant Mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000) and 0.12 M Monosaccharides (0.2 M D-Glucose; 0.2 M D-Mannose; 0.2 M D-Galactose; 0.2 M L-Fucose; 0.2 M D- Xylose; 0.2 M N-Acetyl-D-Glucosamine)

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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: Mar 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.128→120.384 Å / Num. obs: 87793 / % possible obs: 100 % / Redundancy: 40.6 % / CC1/2: 0.997 / Net I/σ(I): 10.5
Reflection shellResolution: 2.128→2.165 Å / Redundancy: 41.9 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4313 / CC1/2: 0.376 / % 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: 2.128→55.086 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 4382 5.02 %
Rwork0.1971 --
obs0.1984 87241 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.128→55.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8154 0 104 588 8846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038566
X-RAY DIFFRACTIONf_angle_d0.6111585
X-RAY DIFFRACTIONf_dihedral_angle_d5.1567199
X-RAY DIFFRACTIONf_chiral_restr0.0441254
X-RAY DIFFRACTIONf_plane_restr0.0031516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1281-2.15230.38191260.36282507X-RAY DIFFRACTION91
2.1523-2.17760.38351390.35442621X-RAY DIFFRACTION96
2.1776-2.20420.3621490.34052700X-RAY DIFFRACTION98
2.2042-2.23210.3721350.33172669X-RAY DIFFRACTION99
2.2321-2.26150.34741320.31062734X-RAY DIFFRACTION99
2.2615-2.29240.27941510.29692729X-RAY DIFFRACTION99
2.2924-2.32520.33351330.29042740X-RAY DIFFRACTION100
2.3252-2.35990.28571330.28572757X-RAY DIFFRACTION100
2.3599-2.39680.2791570.27522717X-RAY DIFFRACTION100
2.3968-2.43610.28341490.26832731X-RAY DIFFRACTION100
2.4361-2.47810.2581110.26132762X-RAY DIFFRACTION100
2.4781-2.52310.31641470.25142731X-RAY DIFFRACTION100
2.5231-2.57170.26271490.2452758X-RAY DIFFRACTION100
2.5717-2.62420.28021590.23242749X-RAY DIFFRACTION100
2.6242-2.68120.23081400.22082741X-RAY DIFFRACTION100
2.6812-2.74360.2251540.21852743X-RAY DIFFRACTION100
2.7436-2.81220.25121400.21322755X-RAY DIFFRACTION100
2.8122-2.88820.22541420.20792772X-RAY DIFFRACTION100
2.8882-2.97320.24811610.21592745X-RAY DIFFRACTION100
2.9732-3.06920.22821700.21282746X-RAY DIFFRACTION100
3.0692-3.17880.23981580.20232756X-RAY DIFFRACTION100
3.1788-3.30610.22661370.20472799X-RAY DIFFRACTION100
3.3061-3.45660.23311560.18642774X-RAY DIFFRACTION100
3.4566-3.63880.19791670.18242779X-RAY DIFFRACTION100
3.6388-3.86670.17941390.1662818X-RAY DIFFRACTION100
3.8667-4.16510.19741410.15232821X-RAY DIFFRACTION100
4.1651-4.58410.16881550.13692829X-RAY DIFFRACTION100
4.5841-5.2470.17531390.15152873X-RAY DIFFRACTION100
5.247-6.60890.20771600.1912909X-RAY DIFFRACTION100
6.6089-55.0860.23031530.18813094X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.2595 Å / Origin y: 54.7948 Å / Origin z: 13.8703 Å
111213212223313233
T0.3117 Å20.0453 Å20.0653 Å2-0.3366 Å20.0217 Å2--0.2863 Å2
L0.98 °20.0673 °2-0.101 °2-1.1332 °20.1289 °2--0.6347 °2
S-0.0824 Å °-0.0521 Å °0.0546 Å °0.1364 Å °0.0807 Å °0.0438 Å °-0.0243 Å °0.054 Å °0.0074 Å °
Refinement TLS groupSelection details: ALL

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