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- PDB-9wed: Plasmodium vivax aspartyl-tRNA synthetase in complex with AMP, As... -

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Basic information

Entry
Database: PDB / ID: 9wed
TitlePlasmodium vivax aspartyl-tRNA synthetase in complex with AMP, Asp-AMP, Partially occupied ASP, Mg ion and Butanetriol
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
(2~{S})-butane-1,2,4-triol / ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE / ADENOSINE MONOPHOSPHATE / ASPARTIC ACID / aspartate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.158 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

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)125,96817
Polymers124,2582
Non-polymers1,71015
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint-108 kcal/mol
Surface area39370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.910, 137.910, 271.743
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 , 7 types, 367 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-0V1 / (2~{S})-butane-1,2,4-triol / (S)-1,2,4-butanentriol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-AMO / ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE


Mass: 462.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N6O10P
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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 Å3/Da / Density % sol: 59.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Morpheus II-G5: 0.1 M Buffer System 5 pH 7.5 (BES, Triethanolamine), 36% Precipitant Mix 5 (30% w/v PEG 3000, 40% v/v 1, 2, 4- Butanetriol, 2% w/v NDSB 256), 100 mM Amino acids II (0.2 M DL- ...Details: Morpheus II-G5: 0.1 M Buffer System 5 pH 7.5 (BES, Triethanolamine), 36% Precipitant Mix 5 (30% w/v PEG 3000, 40% v/v 1, 2, 4- Butanetriol, 2% w/v NDSB 256), 100 mM Amino acids II (0.2 M DL-Arginine hydrochloride, 0.2 M DL- Threonine, 0.2 M DL-Histidine monohydrochloride monohydrate, 0.2 M DL-5-Hydroxylysine hydrochloride, 0.2 M trans-4-hydroxy-L-proline)

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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: Apr 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.158→119.434 Å / Num. obs: 82470 / % possible obs: 100 % / Redundancy: 36.2 % / CC1/2: 1 / Rrim(I) all: 0.129 / Net I/σ(I): 19.4
Reflection shellResolution: 2.158→2.195 Å / Redundancy: 17.2 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4034 / CC1/2: 0.363 / % possible all: 99.8

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Processing

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

9m5m


Resolution: 2.158→59.717 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2163 3986 4.9 %
Rwork0.1892 --
obs0.1906 81415 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.158→59.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8001 0 102 352 8455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068337
X-RAY DIFFRACTIONf_angle_d0.81611270
X-RAY DIFFRACTIONf_dihedral_angle_d3.1096955
X-RAY DIFFRACTIONf_chiral_restr0.0481240
X-RAY DIFFRACTIONf_plane_restr0.0051456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.158-2.18430.3827960.36622044X-RAY DIFFRACTION74
2.1843-2.2120.36481450.34852519X-RAY DIFFRACTION92
2.212-2.24110.37531490.32682715X-RAY DIFFRACTION99
2.2411-2.27180.29781540.29752722X-RAY DIFFRACTION100
2.2718-2.30420.36931280.29842779X-RAY DIFFRACTION100
2.3042-2.33860.29181320.30322770X-RAY DIFFRACTION100
2.3386-2.37520.29961260.26452752X-RAY DIFFRACTION100
2.3752-2.41410.29031340.23582784X-RAY DIFFRACTION100
2.4141-2.45580.24521230.23882764X-RAY DIFFRACTION100
2.4558-2.50040.25031330.2362777X-RAY DIFFRACTION100
2.5004-2.54850.28491580.22462766X-RAY DIFFRACTION100
2.5485-2.60050.23771320.21652772X-RAY DIFFRACTION100
2.6005-2.65710.26581670.2132744X-RAY DIFFRACTION100
2.6571-2.71890.26421490.21222756X-RAY DIFFRACTION100
2.7189-2.78690.24131460.20332769X-RAY DIFFRACTION100
2.7869-2.86220.24941340.20282802X-RAY DIFFRACTION100
2.8622-2.94640.25421390.20542777X-RAY DIFFRACTION100
2.9464-3.04150.25221500.2182787X-RAY DIFFRACTION100
3.0415-3.15020.2461600.20022776X-RAY DIFFRACTION100
3.1502-3.27640.2231430.19432811X-RAY DIFFRACTION100
3.2764-3.42550.25461270.19062806X-RAY DIFFRACTION100
3.4255-3.6060.24411570.18892797X-RAY DIFFRACTION100
3.606-3.83190.19351520.18392838X-RAY DIFFRACTION100
3.8319-4.12770.1591370.1572840X-RAY DIFFRACTION100
4.1277-4.5430.17571510.14052856X-RAY DIFFRACTION100
4.543-5.20.18661510.14672867X-RAY DIFFRACTION100
5.2-6.55020.20711720.18732910X-RAY DIFFRACTION100
6.5502-59.7170.18431410.1893129X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 19.2383 Å / Origin y: 54.268 Å / Origin z: 13.8544 Å
111213212223313233
T0.4286 Å20.0547 Å20.1134 Å2-0.3904 Å20.0042 Å2--0.3645 Å2
L1.2986 °20.2642 °2-0.2771 °2-0.9585 °2-0.0131 °2--0.8295 °2
S0.0094 Å °-0.0739 Å °0.1595 Å °0.1679 Å °0.046 Å °0.0701 Å °-0.0624 Å °0.05 Å °-0.0398 Å °
Refinement TLS groupSelection details: all

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