[English] 日本語
Yorodumi
- PDB-7by6: Plasmodium vivax cytoplasmic Phenylalanyl-tRNA synthetase in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7by6
TitlePlasmodium vivax cytoplasmic Phenylalanyl-tRNA synthetase in complex with BRD1389
Components(Phenylalanyl-tRNA synthetase beta chain, putative) x 2
KeywordsLIGASE / AMINOACYLATION / AMINOACYL-TRNA SYNTHETASE / TRNA-BINDING / ATP-BINDING / AUXILIARY POCKET / HETEROTETRAMERIC
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanyl-tRNA aminoacylation / phenylalanine-tRNA ligase activity / protein heterotetramerization / tRNA binding / magnesium ion binding / RNA binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
Phenylalanine--tRNA ligase beta subunit, B1 domain / Phe-tRNA synthetase beta subunit B1 domain / Phenylalanyl-tRNA synthetase, class IIc, beta subunit, archaeal/eukaryotic type / Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / tRNA synthetase, B5-domain / tRNA synthetase B5 domain / B5 domain profile. ...Phenylalanine--tRNA ligase beta subunit, B1 domain / Phe-tRNA synthetase beta subunit B1 domain / Phenylalanyl-tRNA synthetase, class IIc, beta subunit, archaeal/eukaryotic type / Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / tRNA synthetase, B5-domain / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / B3/4 domain / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / Phenylalanine-tRNA ligase, class IIc, beta subunit / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / B3/4 domain / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / Putative DNA-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / 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) / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FB9 / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.997 Å
AuthorsMalhotra, N. / Manmohan, S. / Harlos, K. / Melillo, B. / Schreiber, S.L. / Manickam, Y. / Sharma, S.
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of malaria parasite phenylalanine tRNA-synthetase inhibition by bicyclic azetidines.
Authors: Sharma, M. / Malhotra, N. / Yogavel, M. / Harlos, K. / Melillo, B. / Comer, E. / Gonse, A. / Parvez, S. / Mitasev, B. / Fang, F.G. / Schreiber, S.L. / Sharma, A.
History
DepositionApr 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._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 / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phenylalanyl-tRNA synthetase beta chain, putative
B: Phenylalanyl-tRNA synthetase beta chain, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4484
Polymers106,8562
Non-polymers5922
Water00
1
A: Phenylalanyl-tRNA synthetase beta chain, putative
B: Phenylalanyl-tRNA synthetase beta chain, putative
hetero molecules

A: Phenylalanyl-tRNA synthetase beta chain, putative
B: Phenylalanyl-tRNA synthetase beta chain, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,8958
Polymers213,7114
Non-polymers1,1844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area20840 Å2
ΔGint-124 kcal/mol
Surface area75420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.523, 74.071, 121.682
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Phenylalanyl-tRNA synthetase beta chain, putative


Mass: 35323.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVX_081300 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: A5K9S0, phenylalanine-tRNA ligase
#2: Protein Phenylalanyl-tRNA synthetase beta chain, putative


Mass: 71532.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVX_090880 / Plasmid: pETM41 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: A5K464, phenylalanine-tRNA ligase
#3: Chemical ChemComp-FB9 / (3S,4R,8R,9R,10S)-N-(4-cyclopropyloxyphenyl)-10-(methoxymethyl)-3,4-bis(oxidanyl)-9-[4-(2-phenylethynyl)phenyl]-1,6-diazabicyclo[6.2.0]decane-6-carboxamide


Mass: 567.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H37N3O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate, 3% w/v poly-gama-glutamic acid (Na+ form, low molecular weight), 3% w/v PEG20000, 0.1 M ammonium sulphate, 0.3 M sodium formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9688 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9688 Å / Relative weight: 1
ReflectionResolution: 2.997→136.5 Å / Num. obs: 25453 / % possible obs: 99.6 % / Redundancy: 6.3 % / CC1/2: 0.921 / Rrim(I) all: 0.145 / Net I/σ(I): 8.5
Reflection shellResolution: 3→3.05 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1186 / CC1/2: 0.741 / Rrim(I) all: 1.288 / % possible all: 94.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.15rc1_3423refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L4G

3l4g


Resolution: 2.997→121.7824 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2882 1296 5.11 %
Rwork0.2137 24079 -
obs0.2176 25375 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 209.44 Å2 / Biso mean: 91.2782 Å2 / Biso min: 47.14 Å2
Refinement stepCycle: final / Resolution: 2.997→121.7824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6873 0 43 0 6916
Biso mean--63.42 --
Num. residues----905
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.997-3.11650.38931300.2935257497
3.1165-3.25840.3951480.27522628100
3.2584-3.43020.32141550.23932618100
3.4302-3.64510.371380.21472650100
3.6451-3.92660.29431430.20912677100
3.9266-4.32170.23931540.18722651100
4.3217-4.94710.24151440.16762698100
4.9471-6.23280.30321470.23262724100
6.2328-121.78240.26741370.2175285999
Refinement TLS params.Method: refined / Origin x: 21.8053 Å / Origin y: 3.5471 Å / Origin z: 25.3067 Å
111213212223313233
T0.7068 Å2-0.0801 Å2-0.072 Å2-0.6935 Å20.0964 Å2--0.6182 Å2
L1.8371 °21.3907 °20.5193 °2-1.434 °20.6892 °2--0.5375 °2
S0.2636 Å °-0.3099 Å °-0.317 Å °0.24 Å °-0.189 Å °-0.2679 Å °0.0629 Å °0.1267 Å °0.0006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA271 - 601
2X-RAY DIFFRACTION1allB0 - 701

+
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