[English] 日本語
Yorodumi
- PDB-2n4x: Structure of the Transmembrane Electron Transporter CcdA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n4x
TitleStructure of the Transmembrane Electron Transporter CcdA
ComponentsCytochrome C-type biogenesis protein (CcdA)
KeywordsMEMBRANE PROTEIN / transmembrane electron transporter / transmembrane reductase / ccda / dsbd homolog
Function / homologymembrane => GO:0016020 / Cytochrome C-type biogenesis protein (CcdA)
Function and homology information
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsChou, J.J. / Williamson, J.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structure and multistate function of the transmembrane electron transporter CcdA.
Authors: Williamson, J.A. / Cho, S.H. / Ye, J. / Collet, J.F. / Beckwith, J.R. / Chou, J.J.
History
DepositionJul 1, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
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: Cytochrome C-type biogenesis protein (CcdA)


Theoretical massNumber of molelcules
Total (without water)22,7711
Polymers22,7711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 75structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Cytochrome C-type biogenesis protein (CcdA)


Mass: 22771.207 Da / Num. of mol.: 1 / Mutation: C16A, C118A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: AF_1057 / Production host: Escherichia coli (E. coli) / Strain (production host): SEN212 / References: UniProt: O29205

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR / Details: Target of the MPSbyNMR consortium of PSI-Biology
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N TROSY-HSQC
1213D TROSY HNCA
1313D TROSY HN(CO)CA
1413D TROSY HN(CA)CO
1513D TROSY HNCO
1613D TROSY HN(CA)CB
1722D 1H-15N TROSY-HSQC
1823D 15N-edited NOESY TROSY-HSQC (60 ms mix time)
1923D 15N-edited NOESY TROSY-HSQC (120 ms mix time)
11023D 13C-edited Methyl NOESY (150 ms mix time)
11114D double 15N-edited NOESY (200 ms mix time)

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 13C; U-100% 15N; U-80% 2H] CcdA-1, 20 mM MES-2, 50 mM sodium chloride-3, 100 mM dodecylphosphocholine-4, 95% H2O/5% D2O95% H2O/5% D2O
20.8 mM [U-100% 13C; U-100% 15N] CcdA-5, 20 mM MES-6, 50 mM sodium chloride-7, 100 mM [U-99% 2H] dodecylphosphocholine-8, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMCcdA-1[U-100% 13C; U-100% 15N; U-80% 2H]1
20 mMMES-21
50 mMsodium chloride-31
100 mMdodecylphosphocholine-41
0.8 mMCcdA-5[U-100% 13C; U-100% 15N]2
20 mMMES-62
50 mMsodium chloride-72
100 mMdodecylphosphocholine-8[U-99% 2H]2
Sample conditionsIonic strength: 0.15 / pH: 6 / Pressure: ambient / Temperature: 303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.38Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.38Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
TopSpin3Bruker Biospincollection
CCPNMRCCPNchemical shift assignment
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 75 / Conformers submitted total number: 15 / Representative conformer: 1

+
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