[English] 日本語
Yorodumi
- PDB-9web: Plasmodium vivax aspartyl-tRNA synthetase in complex with AMP, Py... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9web
TitlePlasmodium vivax aspartyl-tRNA synthetase in complex with AMP, Pyrophosphate, MOPSO and Hexanetriol
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
(2S)-hexane-1,2,6-triol / Chem-6BY / ADENOSINE MONOPHOSPHATE / PYROPHOSPHATE / aspartate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.541 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: aspartate--tRNA ligase
B: aspartate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,69510
Polymers124,2582
Non-polymers1,4378
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10340 Å2
ΔGint-56 kcal/mol
Surface area39710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.698, 138.698, 272.854
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-703-

CL

-
Components

-
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

-
Non-polymers , 6 types, 329 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-6BY / (2R)-2-hydroxy-3-(morpholin-4-yl)propane-1-sulfonic acid


Mass: 225.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-1JW / (2S)-hexane-1,2,6-triol / (-)-1,2,6-Hexanetriol / 6999990


Mass: 134.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Morpheus II-C2: 0.1 M Buffer System 4 pH 6.5 (MOPSO, Bis-Tris), 32.5 Precipitant Mix 6 (25% w/v PEG 4000, 40% w/v 1,2,6-Hexanetriol) and 4 mM Alkalis (0.01 M Rubidium chloride, 0.01 M ...Details: Morpheus II-C2: 0.1 M Buffer System 4 pH 6.5 (MOPSO, Bis-Tris), 32.5 Precipitant Mix 6 (25% w/v PEG 4000, 40% w/v 1,2,6-Hexanetriol) and 4 mM Alkalis (0.01 M Rubidium chloride, 0.01 M Strontium acetate, 0.01 M Cesium acetate, 0.01 M Barium acetate)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 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: 2.54→29.935 Å / Num. obs: 51764 / % possible obs: 99.8 % / Redundancy: 40.3 % / CC1/2: 1 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.016 / Rrim(I) all: 0.106 / Χ2: 1 / Net I/σ(I): 34.1
Reflection shellResolution: 2.54→2.62 Å / % possible obs: 98.6 % / Redundancy: 40.1 % / Rmerge(I) obs: 0.829 / Num. measured all: 174964 / Num. unique obs: 4361 / CC1/2: 0.952 / Rpim(I) all: 0.13 / Rrim(I) all: 0.84 / Χ2: 0.99 / Net I/σ(I) obs: 6.5

-
Processing

Software
NameVersionClassification
PHENIX(1.15rc1_3423: ???)refinement
Aimless0.8.2data scaling
FAST_DP1.6.2data scaling
xia2data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9M5M

9m5m


Resolution: 2.541→29.935 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 2538 4.91 %
Rwork0.1664 --
obs0.1685 51670 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.541→29.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8002 0 89 321 8412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128346
X-RAY DIFFRACTIONf_angle_d1.2211286
X-RAY DIFFRACTIONf_dihedral_angle_d5.7326942
X-RAY DIFFRACTIONf_chiral_restr0.0711231
X-RAY DIFFRACTIONf_plane_restr0.0071440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5413-2.59020.22781370.1812609X-RAY DIFFRACTION98
2.5902-2.6430.28291260.17852698X-RAY DIFFRACTION100
2.643-2.70050.21341380.17952677X-RAY DIFFRACTION100
2.7005-2.76330.24951500.16972672X-RAY DIFFRACTION100
2.7633-2.83230.22121380.17462689X-RAY DIFFRACTION100
2.8323-2.90880.22241410.17092698X-RAY DIFFRACTION100
2.9088-2.99430.25231390.18022677X-RAY DIFFRACTION100
2.9943-3.09090.21941340.17692719X-RAY DIFFRACTION100
3.0909-3.20120.22361600.17782664X-RAY DIFFRACTION100
3.2012-3.32930.23411340.18412720X-RAY DIFFRACTION100
3.3293-3.48060.19051320.17392730X-RAY DIFFRACTION100
3.4806-3.66380.2081380.17312721X-RAY DIFFRACTION100
3.6638-3.89290.22821460.16152724X-RAY DIFFRACTION100
3.8929-4.19270.20281320.14942766X-RAY DIFFRACTION100
4.1927-4.61320.17271490.13212753X-RAY DIFFRACTION100
4.6132-5.27760.19851280.14742797X-RAY DIFFRACTION100
5.2776-6.63730.23011560.18312826X-RAY DIFFRACTION100
6.6373-29.9350.17711600.182992X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.5856 Å / Origin y: 54.3449 Å / Origin z: 13.6652 Å
111213212223313233
T0.3519 Å20.0409 Å20.0954 Å2-0.2743 Å20.0228 Å2--0.2681 Å2
L1.1189 °20.2764 °2-0.1413 °2-1.1439 °2-0.127 °2--0.7129 °2
S-0.0032 Å °-0.0371 Å °0.1439 Å °0.2689 Å °0.039 Å °0.1012 Å °-0.1152 Å °0.0292 Å °-0.0119 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more