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

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Basic information

Entry
Database: PDB / ID: 9wek
TitlePlasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMS in the absence of Mg ions
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: 2.01 Å
AuthorsManickam, Y. / Sharma, V.K. / Pradeepkumar, P.I. / Bagale, S. / 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)125,2775
Polymers124,2582
Non-polymers1,0193
Water11,782654
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-56 kcal/mol
Surface area39580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.465, 140.465, 269.553
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / 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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Morpheus C12: Buffer System 3 pH 8.5 (Tris and BICINE), 37.5% Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350) and 0.09 M NPS (0.3 M Sodium nitrate, 0.3 M Sodium phosphate ...Details: Morpheus C12: Buffer System 3 pH 8.5 (Tris and BICINE), 37.5% Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350) and 0.09 M NPS (0.3 M Sodium nitrate, 0.3 M Sodium phosphate dibasic, 0.3 M Ammonium sulfate)

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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: 2.007→121.646 Å / Num. obs: 105006 / % possible obs: 100 % / Redundancy: 40.9 % / CC1/2: 0.999 / Net I/σ(I): 13.5
Reflection shellResolution: 2.007→2.042 Å / Redundancy: 42.2 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 5153 / CC1/2: 0.353 / % 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
Starting model: 9M5N

9m5n


Resolution: 2.01→50.37 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 5334 5.09 %
Rwork0.179 --
obs0.18 104871 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→50.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8148 0 67 654 8869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038522
X-RAY DIFFRACTIONf_angle_d0.67211534
X-RAY DIFFRACTIONf_dihedral_angle_d4.987152
X-RAY DIFFRACTIONf_chiral_restr0.0451252
X-RAY DIFFRACTIONf_plane_restr0.0041513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.02970.36011890.33023177X-RAY DIFFRACTION98
2.0297-2.05360.34511900.31343205X-RAY DIFFRACTION99
2.0536-2.07860.30251730.28683275X-RAY DIFFRACTION100
2.0786-2.10490.35761730.27513261X-RAY DIFFRACTION100
2.1049-2.13260.31911750.26893270X-RAY DIFFRACTION100
2.1326-2.16190.25851670.2473286X-RAY DIFFRACTION100
2.1619-2.19270.24341650.2413297X-RAY DIFFRACTION100
2.1927-2.22550.22821730.22483266X-RAY DIFFRACTION100
2.2255-2.26030.29761710.22223287X-RAY DIFFRACTION100
2.2603-2.29730.26771800.21983275X-RAY DIFFRACTION100
2.2973-2.33690.24051610.22073293X-RAY DIFFRACTION100
2.3369-2.37940.23781620.20473301X-RAY DIFFRACTION100
2.3794-2.42520.25481830.2053287X-RAY DIFFRACTION100
2.4252-2.47470.23771700.20543284X-RAY DIFFRACTION100
2.4747-2.52850.24931590.2043308X-RAY DIFFRACTION100
2.5285-2.58730.22411880.19883263X-RAY DIFFRACTION100
2.5873-2.6520.22231760.18973347X-RAY DIFFRACTION100
2.652-2.72370.18751800.18543263X-RAY DIFFRACTION100
2.7237-2.80380.20811900.18333303X-RAY DIFFRACTION100
2.8038-2.89430.23051920.18163300X-RAY DIFFRACTION100
2.8943-2.99780.22312000.18493312X-RAY DIFFRACTION100
2.9978-3.11780.19992020.18643289X-RAY DIFFRACTION100
3.1178-3.25970.21871600.17233359X-RAY DIFFRACTION100
3.2597-3.43150.18491680.16423346X-RAY DIFFRACTION100
3.4315-3.64640.17491820.15183341X-RAY DIFFRACTION100
3.6464-3.92780.17071880.1463368X-RAY DIFFRACTION100
3.9278-4.32290.15471770.13313392X-RAY DIFFRACTION100
4.3229-4.9480.14411730.13093423X-RAY DIFFRACTION100
4.948-6.23210.1851750.17583474X-RAY DIFFRACTION100
6.2321-50.3680.18441920.19533685X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 17.4426 Å / Origin y: 55.685 Å / Origin z: 13.5407 Å
111213212223313233
T0.2315 Å20.0224 Å20.0293 Å2-0.3441 Å20.0039 Å2--0.2505 Å2
L1.0052 °20.0266 °2-0.1545 °2-0.778 °20.2499 °2--0.5783 °2
S-0.0165 Å °-0.1372 Å °0.0397 Å °0.0487 Å °0.0037 Å °-0.0067 Å °0.0128 Å °0.0899 Å °0.0104 Å °
Refinement TLS groupSelection details: ALL

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