[English] 日本語
Yorodumi
- PDB-5uj5: Solution structure of the oxidized iron-sulfur protein adrenodoxi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uj5
TitleSolution structure of the oxidized iron-sulfur protein adrenodoxin from Encephalitozoon cuniculi. Seattle Structural Genomics Center for Infectious Disease target EncuA.00705.a
ComponentsAdrenodoxin
KeywordsELECTRON TRANSPORT / infectious diseases / microsporidosis / SSGCID / iron-sulfur protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


mitosome / P450-containing electron transport chain / 2 iron, 2 sulfur cluster binding / mitochondrion / metal ion binding
Similarity search - Function
Adrenodoxin / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Adrenodoxin / Adrenodoxin homolog
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBuchko, G.W. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN2722001200025C United States
CitationJournal: Protein Sci. / Year: 2020
Title: Solution structure for an Encephalitozoon cuniculi adrenodoxin-like protein in the oxidized state.
Authors: Shaheen, S. / Barrett, K.F. / Subramanian, S. / Arnold, S.L.M. / Laureanti, J.A. / Myler, P.J. / Van Voorhis, W.C. / Buchko, G.W.
History
DepositionJan 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.3Feb 26, 2020Group: Database references / Category: citation / citation_author
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
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adrenodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5532
Polymers14,3771
Non-polymers1761
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

-
Components

#1: Protein Adrenodoxin


Mass: 14377.485 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first four residues are part of the N-terminal tag used for NTA purification that remain after cleavage with HRV 3C protease.
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: ECU07_0600 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: M1JK92, UniProt: Q8SV19*PLUS
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic33D 1H-13C NOESY aliphatic
121anisotropic33D 1H-13C NOESY aromatic
131anisotropic33D HN(CA)CB
141anisotropic33D 1H-15N NOESY
151anisotropic33D CBCA(CO)NH
171anisotropic33D HNCO
161anisotropic32D 1H-15N HSQC
181anisotropic32D 1H-13C HSQC aliphatic
191anisotropic32D 1H-13C HSQC aromatic
1101anisotropic1deuterium exchange
1111anisotropic33D C(CO)NH
1121anisotropic13D H(CCO)NH
1131anisotropic32D (HB)CB(CGCD)HD

-
Sample preparation

DetailsType: solution
Contents: 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 1 mM [U-99% 13C; U-99% 15N] E5, 93% H2O/7% D2O
Details: A sample that was only 15N labelled was prepared and used for the deuterium exchange experiment.
Label: sample_1 / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMsodium chloridenatural abundance1
20 mMTRISnatural abundance1
1 mMDTTnatural abundance1
1 mME5[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 0.12 M / Label: condition_1 / pH: 7 / PH err: 0.1 / Pressure: 1 atm / Temperature: 293 K / Temperature err: 0.5

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian VXRSVarianVXRS7503

-
Processing

NMR software
NameVersionDeveloperClassification
Felix2007Accelrys Software Inc.processing
Sparky3.115Goddarddata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
Sparky3.115Goddardpeak picking
PSVS1.5Bhattacharya and Montelionedata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 3
Details: Due to the paramagnetic effects of the iron in the [2Fe-2S] cluster, amides in the close neighbourhood were not observable. These included C54, C60, C63, and C100. Restraints to fix the ...Details: Due to the paramagnetic effects of the iron in the [2Fe-2S] cluster, amides in the close neighbourhood were not observable. These included C54, C60, C63, and C100. Restraints to fix the ligand and the sulfur atoms of these cysteine residues were added based on XRD structures and are contained in ssbond.upl and ssbond.lol.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / 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