[English] 日本語
Yorodumi
- PDB-7ji1: NMR structure of the Streptococcus pyogenes NAD+-glycohydrolase t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ji1
TitleNMR structure of the Streptococcus pyogenes NAD+-glycohydrolase translocation domain
ComponentsADP-ribosyl cyclase / cyclic ADP-ribose hydrolase
KeywordsTOXIN / beta sandwich
Function / homologyNicotine adenine dinucleotide glycohydrolase / NAD glycohydrolase, helical linker domain / Nicotine adenine dinucleotide glycohydrolase (NADase) / Galactose-binding-like domain superfamily / transferase activity / hydrolase activity / ADP-ribosyl cyclase / cyclic ADP-ribose hydrolase
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsVelarde, J.J. / Piai, A. / Chou, J.J. / Wessels, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K08 AI112823 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI130019 United States
CitationJournal: J.Bacteriol. / Year: 2022
Title: Structure of the Streptococcus pyogenes NAD + Glycohydrolase Translocation Domain and Its Essential Role in Toxin Binding to Oropharyngeal Keratinocytes.
Authors: Velarde, J.J. / Piai, A. / Lichtenstein, I.J. / Lynskey, N.N. / Chou, J.J. / Wessels, M.R.
History
DepositionJul 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADP-ribosyl cyclase / cyclic ADP-ribose hydrolase


Theoretical massNumber of molelcules
Total (without water)17,8021
Polymers17,8021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 15015 structures for lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein ADP-ribosyl cyclase / cyclic ADP-ribose hydrolase / N-acetylglucosamine-1-phosphate uridyltransferase / Nicotine adenine dinucleotide glycohydrolase


Mass: 17801.998 Da / Num. of mol.: 1 / Fragment: Translocation domain, residues 38-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: nga, E0F66_06235, GQY31_00740, GTK53_00835 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9R2Y9

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic13D 15N-edited NOESY-TROSY-HSQC
121anisotropic13D 13C-edited NOESY
232anisotropic22D 1H-15N TROSY HSQC
242anisotropic23D TROSY HNCA
252anisotropic23D TROSY HN(CA)CB
262anisotropic23D TROSY HN(CA)CO
272anisotropic23D TROSY HNCO
282anisotropic23D TROSY HN(CO)CA

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-13C; U-15N] NADase translocation domain, 20mM MES, 50mM NaCl, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution20.56 mM [U-13C; U-15N; U-2H] NADase translocation domain, 20mM MES, 80mM NaCl, 0.5mM EDTA, 90% H2O/10% D2Osample_290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMNADase translocation domain[U-13C; U-15N]1
0.56 mMNADase translocation domain[U-13C; U-15N; U-2H]2
20 mMMESnatural abundance1
50 mMNaClnatural abundance1
20 mMMESnatural abundance2
80 mMNaClnatural abundance2
0.5 mMEDTAnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150mM NaCl mMconditions_15.5 ambient 303 K
280mM NaCl mMconditions_25.5 ambient 303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE III HDBrukerAVANCE III HD6002

-
Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CARAKeller and Wuthrichchemical shift assignment
XEASYBartels et al.chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 15 structures for lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 15

+
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://pdbjlvh1.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