[English] 日本語
Yorodumi
- PDB-6b3n: Solution structure of the N-terminal domain of the effector NleG5... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b3n
TitleSolution structure of the N-terminal domain of the effector NleG5-1 from Escherichia coli O157:H7 str. Sakai
ComponentsNleG5-1
KeywordsPROTEIN BINDING / Effector protein / Pathogenesis / Binding domain / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyEffector protein NleG / Effector protein NleG superfamily / Effector protein NleG / biological process involved in symbiotic interaction / ubiquitin-protein transferase activity / T3SS secreted effector NleG
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsValleau, D. / Houliston, S. / Lemak, A. / Anderson, W.F. / Arrowsmith, C. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Solution structure of the N-terminal domain of the effector NleG5-1 from Escherichia coli O157:H7 str. Sakai
Authors: Valleau, D. / Savchenko, A.
History
DepositionSep 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NleG5-1


Theoretical massNumber of molelcules
Total (without water)15,6771
Polymers15,6771
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6690 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein NleG5-1


Mass: 15676.563 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ECs1996, Z2337 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8X4X3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic23D HNCA
141isotropic23D HNCO
151isotropic23D CBCA(CO)NH
191isotropic23D HBHA(CO)NH
181isotropic13D 1H-13C NOESY aliphatic
171isotropic13D 1H-13C NOESY aromatic
161isotropic13D 1H-15N NOESY
1121isotropic13D 1H-13C NOESY aromatic
1101isotropic13D (H)CCH-TOCSY
1111isotropic13D CCH-TOCSY

-
Sample preparation

DetailsType: solution
Contents: 400 uM [U-100% 13C; U-100% 15N] NleG5-1, 15 mM HEPES, 250 mM sodium chloride, 5 mM L-arginine, 5 mM sodium citrate, 1 mM benzamidine, 10 uM DTT, 0.01 % w/v sodium azide, 90% H2O/10% D2O
Label: 13C_15N_double / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMNleG5-1[U-100% 13C; U-100% 15N]1
15 mMHEPESnatural abundance1
250 mMsodium chloridenatural abundance1
5 mML-argininenatural abundance1
5 mMsodium citratenatural abundance1
1 mMbenzamidinenatural abundance1
10 uMDTTnatural abundance1
0.01 % w/vsodium azidenatural abundance1
Sample conditionsIonic strength: 400 mM / Label: condition_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II8001
Bruker AVANCEBrukerAVANCE5002

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ABACUSLemak and Arrowsmithchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 3 / Details: water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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