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- PDB-9wei: Plasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMS... -

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Basic information

Entry
Database: PDB / ID: 9wei
TitlePlasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMS, Divalent metals, MOPSO and Pentanediol
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
Chem-6BX / pentane-1,5-diol / : / 5'-O-(L-alpha-aspartylsulfamoyl)adenosine / aspartate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 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)126,14716
Polymers124,2582
Non-polymers1,88914
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-172 kcal/mol
Surface area39390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.400, 139.400, 273.850
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 , 9 types, 202 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#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
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-9JE / pentane-1,5-diol


Mass: 104.148 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Morpheus II-B3: 0.1 M Buffer System 4 pH 6.5 (MOPSO, Bis-Tris) 30% Precipitant Mix 7 (20% w/v PEG 8000, 40% v/v 1,5- Pentanediol) 2 mM Divalents II (0.005 M Manganese(II) chloride ...Details: Morpheus II-B3: 0.1 M Buffer System 4 pH 6.5 (MOPSO, Bis-Tris) 30% Precipitant Mix 7 (20% w/v PEG 8000, 40% v/v 1,5- Pentanediol) 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, 0.005M 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: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.53→55.23 Å / Num. obs: 53274 / % possible obs: 100 % / Redundancy: 40.4 % / CC1/2: 1 / Net I/σ(I): 10
Reflection shellResolution: 2.53→2.6 Å / Redundancy: 42.5 % / Mean I/σ(I) obs: 0.3 / Num. unique obs: 3871 / CC1/2: 0.94 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
xia2data scaling
xia2data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9M5O

9m5o


Resolution: 2.53→50.35 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 2600 4.92 %
Rwork0.21 --
obs0.212 52808 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.53→50.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7968 0 109 188 8265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038373
X-RAY DIFFRACTIONf_angle_d0.57111347
X-RAY DIFFRACTIONf_dihedral_angle_d21.2963141
X-RAY DIFFRACTIONf_chiral_restr0.0421233
X-RAY DIFFRACTIONf_plane_restr0.0041465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.580.5361090.49252360X-RAY DIFFRACTION90
2.58-2.630.45121560.4182556X-RAY DIFFRACTION98
2.63-2.680.46521370.40422567X-RAY DIFFRACTION99
2.68-2.740.34161260.34522614X-RAY DIFFRACTION100
2.74-2.80.32251180.30112623X-RAY DIFFRACTION100
2.8-2.870.32481320.28072632X-RAY DIFFRACTION100
2.87-2.950.32881290.27872614X-RAY DIFFRACTION100
2.95-3.040.32451330.27732638X-RAY DIFFRACTION100
3.04-3.130.30921320.28182618X-RAY DIFFRACTION100
3.13-3.250.31181400.25792638X-RAY DIFFRACTION100
3.25-3.380.26911340.2452642X-RAY DIFFRACTION100
3.38-3.530.32061620.21312616X-RAY DIFFRACTION100
3.53-3.710.25211430.19292639X-RAY DIFFRACTION100
3.71-3.950.19561260.1812684X-RAY DIFFRACTION100
3.95-4.250.23181450.15752667X-RAY DIFFRACTION100
4.25-4.680.18411400.14632694X-RAY DIFFRACTION100
4.68-5.360.19941430.16722720X-RAY DIFFRACTION100
5.36-6.740.23491400.21912755X-RAY DIFFRACTION100
6.75-50.350.23571550.20452931X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.5646 Å / Origin y: 54.6618 Å / Origin z: 13.5227 Å
111213212223313233
T0.7329 Å20.0278 Å20.0959 Å2-0.7019 Å20.0212 Å2--0.6739 Å2
L1.3835 °20.1998 °2-0.2485 °2-1.3383 °20.1683 °2--0.9376 °2
S-0.0234 Å °-0.0963 Å °0.1626 Å °0.2062 Å °0.056 Å °0.0703 Å °-0.1058 Å °0.1314 Å °-0 Å °
Refinement TLS groupSelection details: all

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