BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 16674

Title: NMR Solution structures of fully reduced cytochrome c3 from Desulfovibrio desulfuricans ATCC 2777   PubMed: 20886839

Deposition date: 2010-01-13 Original release date: 2010-10-18

Authors: Turner, David; Paixao, Vitor

Citation: Paixao, Vitor; Vis, Hans; Turner, David. "Redox linked conformational changes in cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774."  Biochemistry 49, 9620-9629 (2010).

Assembly members:
cytochrome_c3, polymer, 107 residues, 11383.284 Da.
HEM, non-polymer, 616.487 Da.

Natural source:   Common Name: Desulfovibrio desulfuricans   Taxonomy ID: 876   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Desulfovibrio desulfuricans

Experimental source:   Production method: purified from the natural source   Host organism: Desulfovibrio desulfuricans   Vector: na

Entity Sequences (FASTA):
cytochrome_c3: APAVPDKPVEVKGSQKTVMF PHAPHEKVECVTCHHLVDGK ESYAKCGSSGCHDDLTAKKG EKSLYYVVHARGELKHTSCL ACHSKVVAEKPELKKDLTGC AKSKCHP

Data sets:
Data typeCount
1H chemical shifts634

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1cytochrome c31
2HEM 12
3HEM 22
4HEM 32
5HEM 42

Entities:

Entity 1, cytochrome c3 107 residues - 11383.284 Da.

1   ALAPROALAVALPROASPLYSPROVALGLU
2   VALLYSGLYSERGLNLYSTHRVALMETPHE
3   PROHISALAPROHISGLULYSVALGLUCYS
4   VALTHRCYSHISHISLEUVALASPGLYLYS
5   GLUSERTYRALALYSCYSGLYSERSERGLY
6   CYSHISASPASPLEUTHRALALYSLYSGLY
7   GLULYSSERLEUTYRTYRVALVALHISALA
8   ARGGLYGLULEULYSHISTHRSERCYSLEU
9   ALACYSHISSERLYSVALVALALAGLULYS
10   PROGLULEULYSLYSASPLEUTHRGLYCYS
11   ALALYSSERLYSCYSHISPRO

Entity 2, HEM 1 - C34 H32 Fe N4 O4 - 616.487 Da.

1   HEM

Samples:

sample_1: cytochrome c31.85 – 2.0 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.1 M; pH: 6.46; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1

Software:

xwinnmr, Bruker Biospin - data analysis, processing

TOPSPIN, Bruker Biospin - data analysis, processing

XEASY, Bartels et al. - chemical shift assignment, peak picking

PARADYANA, (INDYANA) Turner et al. - refinement, structure solution

SPARKY, Goddard - chemical shift assignment, peak picking

Molmol, Koradi, Billeter and Wuthrich - rms and mean structure calculations, superimposition, visual inspection

NMR spectrometers:

  • Bruker DRX 500 MHz
  • Bruker Avance 800 MHz

Related Database Links:

BMRB 16443
PDB
GB AAF43894 ACL49909
REF WP_012625633