[English] 日本語
Yorodumi
- PDB-1qn1: SOLUTION STRUCTURE OF DESULFOVIBRIO GIGAS FERRICYTOCHROME C3, NMR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qn1
TitleSOLUTION STRUCTURE OF DESULFOVIBRIO GIGAS FERRICYTOCHROME C3, NMR, 15 STRUCTURES
ComponentsCYTOCHROME C3
KeywordsELECTRON TRANSPORT / HEMEPROTEIN / CYTOCHROME C3 / REDOX COOPERATIVITY / REDOX-BOHR COOPERATIVITY / ENERGY TRANSDUCTION / PARAMAGNETIC
Function / homology
Function and homology information


anaerobic respiration / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Class III cytochrome C / Class III cytochrome C family / Cytochrome c, class III / Cytochrome C3 / Cytochrome C3 / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
HEME C / Cytochrome c3
Similarity search - Component
Biological speciesDESULFOVIBRIO GIGAS (bacteria)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS WITH SIMULATED ANNEALING
AuthorsBrennan, L. / Messias, A.C. / Legall, J. / Turner, D.L. / Xavier, A.V.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Structural Basis for the Network of Functional Cooperativities in Cytochromes C3 from Desulfovibrio Gigas: Solution Structures of the Oxidised and Reduced States
Authors: Brennan, L. / Turner, D.L. / Messias, A.C. / Teodoro, M.L. / Legall, J. / Santos, H. / Xavier, A.V.
#1: Journal: Biochemistry / Year: 1998
Title: Functional and Mechanistic Studies of Cytochrome C3 from Desulfovibrio Gigas: Thermodynamics of a 'Proton Thruster'
Authors: Louro, R.O. / Catarino, T. / Turner, D.L. / Picarra-Pereira, M.A. / Pacheco, I. / Legall, J. / Xavier, A.V.
#2: Journal: Protein Sci. / Year: 1996
Title: Cytochromes C3 from Desulfovibrio Gigas: Crystal Structure at 1.8 A Resolution and Evidence for a Specific Calcium-Binding Site
Authors: Matias, P.M. / Morais, J. / Carrondo, M.A. / Wilson, K. / Dauter, Z. / Sieker, L.
History
DepositionOct 11, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_mr / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4915
Polymers12,0171
Non-polymers2,4744
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 / 600LEAST RESTRAINT VIOLATION
RepresentativeModel #1

-
Components

#1: Protein CYTOCHROME C3 / TETRAHEME CYTOCHROME


Mass: 12016.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CLASS III OF C-TYPE CYTOCHROMES, FULLY OXIDISED FORM
Source: (natural) DESULFOVIBRIO GIGAS (bacteria) / Cellular location: PERIPLASM / References: UniProt: P00133
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
Has protein modificationY
Sequence detailsRESIDUE 40 WAS FOUND TO BE GLN

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-1H-NOESY
1212D-1H-TOCSY
1312D-1H-COSY

-
Sample preparation

Sample conditionspH: 5.1 / Temperature: 306.4 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

-
Processing

NMR software
NameDeveloperClassification
PARADYANAD.L.TURNER,L.BRENNAN,S.G.CHAMBERLIN, R.O.LOURO, A.V.XAVIERrefinement
PARADYANAstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS WITH SIMULATED ANNEALING / Software ordinal: 1
Details: DIPOLAR SHIFTS WERE USED AS RESTRAINTS IN AN EXTENDED VERSION OF DYANA CALLED PARADYANA. D.L.TURNER,L,BRENNAN,S.G.CHAMBERLIN, R.O.LOURO,A.V.XAVIER (1998)DETERMINATION OF SOLUTION STRUCTURES ...Details: DIPOLAR SHIFTS WERE USED AS RESTRAINTS IN AN EXTENDED VERSION OF DYANA CALLED PARADYANA. D.L.TURNER,L,BRENNAN,S.G.CHAMBERLIN, R.O.LOURO,A.V.XAVIER (1998)DETERMINATION OF SOLUTION STRUCTURES OF PARAMAGNETIC PROTEINS BY NMR.EUR.BIOPHYS.J.27,367-375.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 600 / 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://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