[English] 日本語
Yorodumi
- PDB-1clf: CLOSTRIDIUM PASTEURIANUM FERREDOXIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1clf
TitleCLOSTRIDIUM PASTEURIANUM FERREDOXIN
ComponentsFERREDOXIN
KeywordsELECTRON TRANSFER (IRON-SULFUR PROTEIN)
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding / cytoplasm
Similarity search - Function
7Fe ferredoxin / 4Fe-4S binding domain / Alpha-Beta Plaits - #20 / : / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits ...7Fe ferredoxin / 4Fe-4S binding domain / Alpha-Beta Plaits - #20 / : / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesClostridium pasteurianum (bacteria)
MethodSOLUTION NMR
AuthorsBertini, I. / Donaire, A. / Feinberg, B.A. / Luchinat, C. / Piccioli, M. / Yuan, H.
Citation
Journal: Eur.J.Biochem. / Year: 1995
Title: Solution structure of the oxidized 2[4Fe-4S] ferredoxin from Clostridium pasteurianum.
Authors: Bertini, I. / Donaire, A. / Feinberg, B.A. / Luchinat, C. / Piccioli, M. / Yuan, H.
#1: Journal: J.Am.Chem.Soc. / Year: 1994
Title: The Fe4S4 Centers in Ferredoxins Studied Through Proton and Carbon Hyperfine Coupling. Sequence Specific Assignments of Cysteines in Ferredoxins from Clostridium Acidi Urici and Clostridium Pasteurianum
Authors: Bertini, I. / Cappozzi, F. / Luchinat, C. / Piccioli, M. / Vila, A.J.
#2: Journal: Biochemistry / Year: 1994
Title: Comparison of Native and Mutant Proteins Provides a Sequence-Specific Assignment of the Cysteinyl Ligand Proton NMR Resonances in the 2[Fe4S4] Ferredoxin from Clostridium Pasteurianum
Authors: Scrofani, S.D.B. / Brereton, P.S. / Hamer, A.M. / Lavery, M.J. / Mcdowall, S.G. / Vincent, G.A. / Brownlee, R.T.C. / Hoogenraad, N.J. / Sadek, M. / Wedd, A.G.
#3: Journal: Methods Enzymol. / Year: 1972
Title: Preparation and Properties of Clostridial Ferredoxins
Authors: Rabinowitz, J.
History
DepositionJun 21, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2033
Polymers5,5001
Non-polymers7032
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: VAL 53 - GLN 54 MODEL 1 OMEGA = 221.48 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: GLN 54 - GLU 55 MODEL 1 OMEGA = 146.66 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: VAL 53 - GLN 54 MODEL 2 OMEGA = 211.62 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: TYR 2 - LYS 3 MODEL 3 OMEGA = 146.71 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: VAL 53 - GLN 54 MODEL 3 OMEGA = 215.45 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
6: TYR 2 - LYS 3 MODEL 4 OMEGA = 135.35 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: VAL 53 - GLN 54 MODEL 4 OMEGA = 216.57 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
8: TYR 2 - LYS 3 MODEL 5 OMEGA = 143.38 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
9: LYS 3 - ILE 4 MODEL 5 OMEGA = 147.43 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
10: GLY 41 - ASN 42 MODEL 5 OMEGA = 212.47 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
11: VAL 53 - GLN 54 MODEL 5 OMEGA = 220.84 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
12: GLN 54 - GLU 55 MODEL 5 OMEGA = 135.31 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
13: TYR 2 - LYS 3 MODEL 6 OMEGA = 144.67 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
14: LYS 3 - ILE 4 MODEL 6 OMEGA = 146.53 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
15: GLY 41 - ASN 42 MODEL 6 OMEGA = 212.28 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
16: VAL 53 - GLN 54 MODEL 6 OMEGA = 235.88 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
17: TYR 2 - LYS 3 MODEL 7 OMEGA = 140.71 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
18: VAL 53 - GLN 54 MODEL 7 OMEGA = 263.66 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
19: TYR 2 - LYS 3 MODEL 8 OMEGA = 141.08 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
20: VAL 53 - GLN 54 MODEL 8 OMEGA = 238.60 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
21: ALA 1 - TYR 2 MODEL 9 OMEGA = 142.99 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
22: VAL 53 - GLN 54 MODEL 9 OMEGA = 241.31 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
23: TYR 2 - LYS 3 MODEL 10 OMEGA = 145.78 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
24: VAL 53 - GLN 54 MODEL 10 OMEGA = 227.60 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
25: GLN 54 - GLU 55 MODEL 10 OMEGA = 131.81 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
26: VAL 53 - GLN 54 MODEL 11 OMEGA = 231.51 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
27: TYR 2 - LYS 3 MODEL 12 OMEGA = 149.84 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
28: VAL 53 - GLN 54 MODEL 12 OMEGA = 229.62 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
29: TYR 2 - LYS 3 MODEL 13 OMEGA = 148.48 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
30: VAL 53 - GLN 54 MODEL 13 OMEGA = 226.49 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
31: GLN 54 - GLU 55 MODEL 13 OMEGA = 144.75 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
32: TYR 2 - LYS 3 MODEL 14 OMEGA = 145.89 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
33: LYS 3 - ILE 4 MODEL 14 OMEGA = 148.07 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
34: VAL 53 - GLN 54 MODEL 14 OMEGA = 231.16 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
35: TYR 2 - LYS 3 MODEL 15 OMEGA = 144.88 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
36: VAL 53 - GLN 54 MODEL 15 OMEGA = 246.86 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
37: TYR 2 - LYS 3 MODEL 16 OMEGA = 146.32 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
38: VAL 53 - GLN 54 MODEL 16 OMEGA = 226.46 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
39: GLN 54 - GLU 55 MODEL 16 OMEGA = 144.95 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / -
Representative

-
Components

#1: Protein FERREDOXIN


Mass: 5500.159 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Clostridium pasteurianum (bacteria) / Strain: WINOGRADSKY / References: UniProt: P00195
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other

-
Processing

NMR software
NameVersionDeveloperClassification
DIANAGUNTERT,BRAUN,WUTHRICHrefinement
Amber4PEARLMAN,CASE,CALDWELL,SIEBEL,SINGH,WEINER,KOLLMANrefinement
NMR ensembleConformers submitted total number: 16

+
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