[English] 日本語
Yorodumi
- PDB-2ndo: Structure of EcDsbA-sulfonamide1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ndo
TitleStructure of EcDsbA-sulfonamide1 complex
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASES / Oxidised EcDsbA / Sulfonamide
Function / homology
Function and homology information


cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / outer membrane-bounded periplasmic space
Similarity search - Function
Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-{[(4-iodophenyl)sulfonyl]amino}benzoic acid / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model6
AuthorsWilliams, M.L. / Doak, B.C. / Vazirani, M. / Ilyichova, O. / Wang, G. / Bermel, W. / Simpson, J.S. / Chalmers, D.K. / King, G.F. / Mobli, M. / Scanlon, M.J.
CitationJournal: J.Biomol.Nmr / Year: 2016
Title: Determination of ligand binding modes in weak protein-ligand complexes using sparse NMR data.
Authors: Mohanty, B. / Williams, M.L. / Doak, B.C. / Vazirani, M. / Ilyichova, O. / Wang, G. / Bermel, W. / Simpson, J.S. / Chalmers, D.K. / King, G.F. / Mobli, M. / Scanlon, M.J.
History
DepositionAug 22, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_site
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_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5582
Polymers21,1551
Non-polymers4031
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 21155.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AEG4
#2: Chemical ChemComp-SFQ / 2-{[(4-iodophenyl)sulfonyl]amino}benzoic acid


Mass: 403.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10INO4S

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2123D F1- 13 C, 15 N-filtered, F3 - 13 C ali (methyl) edited [ 1 H, 1 H]-NOESY
2222D F1-edited, F2-13C,15N-Filtered [1H,1H]-NOESY
2322D 1H-13C HSQC
1412D 1H-13C HSQC
1513D CHD2-C-TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.35 mM Isotopomer sample Oxidised EcDsbA, 95% H2O/5% D2O95% H2O/5% D2O
20.4 mM [U-99% 13C; U-99% 15N] Oxidised EcDsbA, 1.5 mM Sulfonamide1, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.35 mMOxidised EcDsbA-1Isotopomer sample1
0.4 mMOxidised EcDsbA-2[U-99% 13C; U-99% 15N]2
1.5 mMSulfonamide1-32
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 6.8 ambient atm300 K
250 6.8 ambient atm300 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE6003

-
Processing

NMR software
NameVersionDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
HADDOCK2.1Alexandre Bonvinrigid body docking
HADDOCK2.1Alexandre Bonvinsimulated annealing
HADDOCK2.1Alexandre Bonvinwater refinement
HADDOCKrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The released PDB entry 1FVK was used for HADDOCK model building
NMR constraintsNOE constraints total: 19
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 6

+
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