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 15301

Title: Solution model of crosslinked complex of cytochrome c and adrenodoxin   PubMed: 18439013

Authors: Xu, Xingfu; Reinle, Wolfgang; Hannemann, Frank; Konarev, Peter; Svergun, Dmitri; Bernhardt, Rita; Ubbink, Marcellus

Citation: Xu, Xingfu; Reinle, Wolfgang; Hannemann, Frank; Konarev, Peter; Svergun, Dmitri; Bernhardt, Rita; Ubbink, Marcellus. "Dynamics in a pure encounter complex of two proteins studied by solution scattering and paramagnetic NMR spectroscopy"  J. Am. Chem. Soc. 130, 6395-6403 (2008).

Assembly members:
Cytc, polymer, 108 residues, Formula weight is not available
Adx, polymer, 105 residues, Formula weight is not available
HEME C, non-polymer, 618.503 Da.
FE2/S2 (INORGANIC) CLUSTER, non-polymer, 175.820 Da.

Natural source:   Common Name: baker   Taxonomy ID: 4932   Superkingdom: not available   Kingdom: not available   Genus/species: Eukaryota Fungi

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
Cytc: TEFKAGSAKKGATLFKTRCL QCHTVEKGGPHKCGPNLHGI FGRHSGQAEGYSYTDANIKK NVLWDENNMSEYLTNPKKYI PGTKMAFGGLKKEKDRNDLI TYLKKATE
Adx: EDKITVHFINRDGETLTTKG KIGDSLLDVVVQNNLDIDGF GACEGTLACSTCHLIFEQHI FEKLEAITDEENDMLDCAYG LTDRSRLGCQISLTKAMDNM TVRVP

Data sets:
Data typeCount
15N chemical shifts146
1H chemical shifts146

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1CcV28C1
2AdxL80C2
3HEME C3
4FE2/S2 (INORGANIC) CLUSTER4

Entities:

Entity 1, CcV28C 108 residues - Formula weight is not available

Residues -4-0 represent a non-native tag

1   THRGLUPHELYSALAGLYSERALALYSLYS
2   GLYALATHRLEUPHELYSTHRARGCYSLEU
3   GLNCYSHISTHRVALGLULYSGLYGLYPRO
4   HISLYSCYSGLYPROASNLEUHISGLYILE
5   PHEGLYARGHISSERGLYGLNALAGLUGLY
6   TYRSERTYRTHRASPALAASNILELYSLYS
7   ASNVALLEUTRPASPGLUASNASNMETSER
8   GLUTYRLEUTHRASNPROLYSLYSTYRILE
9   PROGLYTHRLYSMETALAPHEGLYGLYLEU
10   LYSLYSGLULYSASPARGASNASPLEUILE
11   THRTYRLEULYSLYSALATHRGLU

Entity 2, AdxL80C 105 residues - Formula weight is not available

The first two residues have no coordinates in AYF

1   GLUASPLYSILETHRVALHISPHEILEASN
2   ARGASPGLYGLUTHRLEUTHRTHRLYSGLY
3   LYSILEGLYASPSERLEULEUASPVALVAL
4   VALGLNASNASNLEUASPILEASPGLYPHE
5   GLYALACYSGLUGLYTHRLEUALACYSSER
6   THRCYSHISLEUILEPHEGLUGLNHISILE
7   PHEGLULYSLEUGLUALAILETHRASPGLU
8   GLUASNASPMETLEUASPCYSALATYRGLY
9   LEUTHRASPARGSERARGLEUGLYCYSGLN
10   ILESERLEUTHRLYSALAMETASPASNMET
11   THRVALARGVALPRO

Entity 3, HEME C - C34 H34 Fe N4 O4 - 618.503 Da.

1   HEC

Entity 4, FE2/S2 (INORGANIC) CLUSTER - Fe2 S2 - 175.820 Da.

1   FES

Samples:

CcV28C_AdxL80C: CcV28C, [U-98% 15N], 0.2 – 0.6 mM; AdxL80C0.2 – 0.6 mM; potassium phosphate 20 mM

AdxL80C_CcV28C: AdxL80C, [U-98% 15N], 0.2 – 0.6 mM; CcV28C0.2 – 0.6 mM; potassium phosphate 20 mM

CcV28C: CcV28C, [U-98% 15N], 1.0 mM; DTT 5 mM; potassium phosphate 20 mM

AdxL80C: AdxL80C, [U-98% 15N], 0.5 – 0.8 mM; DTT 5 mM; potassium phosphate 20 mM

sample_conditions_1: pH: 7.4; pressure: 1 atm; temperature: 285 K

sample_conditions_2: ionic strength: 0.4 M; pH: 7.4; pressure: 1 atm; temperature: 301 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCCcV28C_AdxL80Cisotropicsample_conditions_1
2D 1H-15N HSQCAdxL80C_CcV28Cisotropicsample_conditions_1
3D 1H-15N NOESYCcV28C_AdxL80Cisotropicsample_conditions_2
3D 1H-15N NOESYAdxL80C_CcV28Cisotropicsample_conditions_2
2D 1H-15N HSQCCcV28Cisotropicsample_conditions_1
2D 1H-15N HSQCAdxL80Cisotropicsample_conditions_1
3D 1H-15N NOESYAdxL80Cisotropicsample_conditions_1
3D 1H-15N TOCSYAdxL80Cisotropicsample_conditions_1

Software:

AZARA, Boucher - processing

ANSIG, Kraulis - data analysis

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

  • Bruker DMX 600 MHz

Related Database Links:

PDB
BMRB 131 17845 17846 17903 17904 19638 4566 7390
DBJ GAA24396 BAA00362 BAA00363
EMBL CAA24605 CAA89576 CAY80764
GB AAA62856 AAA88751 AAB59344 AHY79034 AJP39735 AAA30357 AAA30358 AAB21264 AAI09850 ABQ13041
PRF 1409323A
REF NP_012582 NP_851354 XP_005889885 XP_010861227
SP P00044 P00257
TPG DAA08835 DAA22428