[English] 日本語
Yorodumi
- PDB-7vc2: Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vc2
TitleToxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L96 and L-proline in space group P21
ComponentsProlyl-tRNA synthetase (ProRS)
KeywordsLIGASE/LIGASE INHIBITOR / PROTEIN TRANSLATION / INHIBITOR / PRS / ATP POCKET / LIGASE / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / aminoacyl-tRNA deacylase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / Proline-tRNA ligase, class IIa / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II ...YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / Proline-tRNA ligase, class IIa / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / 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)
Similarity search - Domain/homology
Chem-1UI / PROLINE / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.096 Å
AuthorsYogavel, M. / Malhotra, N. / Sharma, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)PR32713 India
CitationJournal: Plos Pathog. / Year: 2023
Title: Targeting prolyl-tRNA synthetase via a series of ATP-mimetics to accelerate drug discovery against toxoplasmosis.
Authors: Yogavel, M. / Bougdour, A. / Mishra, S. / Malhotra, N. / Chhibber-Goel, J. / Bellini, V. / Harlos, K. / Laleu, B. / Hakimi, M.A. / Sharma, A.
History
DepositionSep 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prolyl-tRNA synthetase (ProRS)
B: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,88419
Polymers115,8752
Non-polymers2,01017
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-3 kcal/mol
Surface area38290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.100, 81.620, 104.880
Angle α, β, γ (deg.)90.000, 102.680, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Prolyl-tRNA synthetase (ProRS)


Mass: 57937.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGRH88_057780 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J6JUK2

-
Non-polymers , 5 types, 433 molecules

#2: Chemical ChemComp-1UI / 4-[(3S)-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(5-methoxypyridin-3-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide


Mass: 499.536 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H26FN5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.12 M Ethylene glycols (0.3M Diethylene glycol, 0.3M Triethylene glycol, 0.3M Tetraethylene glycol, 0.3M Pentaethylene glycol), 0.1 M Buffer (Imidazole; MES monohydrate), 30% v/v ...Details: 0.12 M Ethylene glycols (0.3M Diethylene glycol, 0.3M Triethylene glycol, 0.3M Tetraethylene glycol, 0.3M Pentaethylene glycol), 0.1 M Buffer (Imidazole; MES monohydrate), 30% v/v Precipitant Mix (40% v/v Ethylene glycol, 20% w/v PEG 8000)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.096→47.42 Å / Num. obs: 145446 / % possible obs: 99.6 % / Redundancy: 6.9 % / CC1/2: 1 / Net I/σ(I): 13.5
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 22375 / CC1/2: 0.74

-
Processing

Software
NameVersionClassification
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XIF

5xif


Resolution: 2.096→47.42 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.218 7280 5.01 %
Rwork0.1771 138166 -
obs0.1791 145446 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.16 Å2 / Biso mean: 51.4103 Å2 / Biso min: 29.29 Å2
Refinement stepCycle: final / Resolution: 2.096→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7635 0 139 418 8192
Biso mean--63.49 54.1 -
Num. residues----947
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.096-2.11950.31192030.3224384183
2.1195-2.14450.38322480.29844720100
2.1445-2.17060.32052360.28064500100
2.1706-2.19810.32262450.28584710100
2.1981-2.2270.32332410.27784604100
2.227-2.25750.30262460.27074663100
2.2575-2.28980.28712430.25314588100
2.2898-2.32390.29472410.25114636100
2.3239-2.36030.32562460.24484639100
2.3603-2.3990.26452420.24314652100
2.399-2.44030.26522440.22464626100
2.4403-2.48470.27492450.21054629100
2.4847-2.53250.24082430.20914634100
2.5325-2.58420.27162410.20034601100
2.5842-2.64040.2712430.19424636100
2.6404-2.70180.25392410.19024659100
2.7018-2.76930.25452480.18694648100
2.7693-2.84420.24152440.18984601100
2.8442-2.92790.23992500.1924650100
2.9279-3.02240.24792460.19274624100
3.0224-3.13040.23882420.17934611100
3.1304-3.25570.21272430.17734611100
3.2557-3.40380.23212490.17364712100
3.4038-3.58320.19952430.16564579100
3.5832-3.80760.18412440.15564606100
3.8076-4.10150.18522460.14384664100
4.1015-4.51390.16482450.13734639100
4.5139-5.16640.17042420.12734625100
5.1664-6.50640.19892480.16394614100
6.5064-47.420.17852420.164644100
Refinement TLS params.Method: refined / Origin x: 14.8761 Å / Origin y: 1.0008 Å / Origin z: 33.7923 Å
111213212223313233
T0.3961 Å2-0.0278 Å2-0.0011 Å2-0.3426 Å2-0.0159 Å2--0.4143 Å2
L0.6828 °20.0199 °2-0.076 °2-0.3519 °20.176 °2--1.0596 °2
S-0.0257 Å °0.0757 Å °-0.0761 Å °0.0403 Å °-0.0475 Å °0.0108 Å °0.1665 Å °-0.0699 Å °0 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