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- PDB-9m5o: Plasmodium vivax aspartyl-tRNA synthetase in complex with asparty... -

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Basic information

Entry
Database: PDB / ID: 9m5o
TitlePlasmodium vivax aspartyl-tRNA synthetase in complex with aspartyl sulfamoyl adenosine (Asp-AMS) Complex
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 / aspartate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.839 Å
AuthorsSharma, V.K. / Manickam, Y. / Sharma, A. / Bagale, S. / Pradeepkumar, P.I.
Funding support India, 3items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)CRG/2023/004351 India
Indian Council of Medical ResearchCAR-2024-01-000140 India
Department of Biotechnology (DBT, India)PR32713 India
CitationJournal: To Be Published
Title: Natural product-mediated reaction hijacking mechanism validates Plasmodium aspartyl-tRNA synthetase as an antimalarial drug target
Authors: Ketprasit, N. / Tai, C.W. / Sharma, V.K. / Manickam, Y. / Khandokar, Y. / Ye, W. / Dogovski, C. / Hilko, D.H. / Morton, C. / Braun, A.S.C. / Leeming, M. / Bagale, S. / Pradeepkumar, P.I. / ...Authors: Ketprasit, N. / Tai, C.W. / Sharma, V.K. / Manickam, Y. / Khandokar, Y. / Ye, W. / Dogovski, C. / Hilko, D.H. / Morton, C. / Braun, A.S.C. / Leeming, M. / Bagale, S. / Pradeepkumar, P.I. / Panjikar, S. / Poulsen, S.A. / Griffin, M.D.W. / Sharma, A. / Tilley, L. / Xie, S.C.
History
DepositionMar 6, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 2025Provider: 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)125,2788
Polymers124,2582
Non-polymers1,0206
Water15,997888
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-74 kcal/mol
Surface area39080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.253, 140.253, 267.611
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-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.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 888 / 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: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium acetate trihydrate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350, PvAspRS-Asp-AMS 0.06M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 0.1M Buffer ...Details: 0.2M Sodium acetate trihydrate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350, PvAspRS-Asp-AMS 0.06M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 0.1M Buffer System (Tris (base) and BICINE) pH 8.5, 30% v/v Precipitant Mix (40% v/v PEG 500 MME and 20% w/v PEG 20000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.839→121.46 Å / Num. obs: 134470 / % possible obs: 100 % / Redundancy: 39.3 % / CC1/2: 1 / Rmerge(I) obs: 0.22 / Rrim(I) all: 0.223 / Net I/σ(I): 14.7
Reflection shellResolution: 1.839→1.87 Å / Rmerge(I) obs: 5.537 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 6630 / CC1/2: 0.366 / Rrim(I) all: 5.653 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.15rc1_3423: ???)refinement
autoPROCdata scaling
PHASERphasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.839→50.201 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1956 6602 4.91 %
Rwork0.1677 --
obs0.1691 134353 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.839→50.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8117 0 66 888 9071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088488
X-RAY DIFFRACTIONf_angle_d0.96111482
X-RAY DIFFRACTIONf_dihedral_angle_d5.1527172
X-RAY DIFFRACTIONf_chiral_restr0.0551248
X-RAY DIFFRACTIONf_plane_restr0.0061505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8392-1.86010.36652060.34434125X-RAY DIFFRACTION98
1.8601-1.8820.33072120.32164210X-RAY DIFFRACTION100
1.882-1.90490.30372180.28034154X-RAY DIFFRACTION100
1.9049-1.92910.30172280.27924201X-RAY DIFFRACTION100
1.9291-1.95440.27542070.24964214X-RAY DIFFRACTION100
1.9544-1.98120.30421950.22194216X-RAY DIFFRACTION100
1.9812-2.00950.21662110.20994224X-RAY DIFFRACTION100
2.0095-2.03950.21782050.19374223X-RAY DIFFRACTION100
2.0395-2.07140.20612080.19454216X-RAY DIFFRACTION100
2.0714-2.10540.2162200.19394175X-RAY DIFFRACTION100
2.1054-2.14170.23872350.18314230X-RAY DIFFRACTION100
2.1417-2.18060.21492230.17824191X-RAY DIFFRACTION100
2.1806-2.22250.19872130.17114241X-RAY DIFFRACTION100
2.2225-2.26790.20472170.1714234X-RAY DIFFRACTION100
2.2679-2.31720.2092280.16774202X-RAY DIFFRACTION100
2.3172-2.37110.1862190.15924228X-RAY DIFFRACTION100
2.3711-2.43040.20022230.16044241X-RAY DIFFRACTION100
2.4304-2.49610.17792170.164241X-RAY DIFFRACTION100
2.4961-2.56960.18772390.16564227X-RAY DIFFRACTION100
2.5696-2.65250.19262340.15984228X-RAY DIFFRACTION100
2.6525-2.74730.18052310.16214252X-RAY DIFFRACTION100
2.7473-2.85730.20532090.16324278X-RAY DIFFRACTION100
2.8573-2.98730.21212150.16574288X-RAY DIFFRACTION100
2.9873-3.14480.19152290.16444264X-RAY DIFFRACTION100
3.1448-3.34180.17732430.16454297X-RAY DIFFRACTION100
3.3418-3.59970.18962180.15514306X-RAY DIFFRACTION100
3.5997-3.96190.17341940.14164359X-RAY DIFFRACTION100
3.9619-4.53480.14262290.12534386X-RAY DIFFRACTION100
4.5348-5.71210.18462240.14664428X-RAY DIFFRACTION100
5.7121-50.2010.19972520.18524672X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 17.8289 Å / Origin y: 55.9617 Å / Origin z: 13.8792 Å
111213212223313233
T0.1376 Å20.0227 Å20.0201 Å2-0.1914 Å20.0209 Å2--0.1472 Å2
L0.5677 °2-0.0088 °2-0.0578 °2-0.5199 °20.1823 °2--0.4407 °2
S-0.0286 Å °-0.0273 Å °0.0124 Å °0.0059 Å °0.02 Å °-0.0146 Å °0.0163 Å °0.0447 Å °0.0047 Å °
Refinement TLS groupSelection details: all

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