BMRB Entry 25908

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR25908
MolProbity Validation Chart

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NMR-STAR v3 text file.
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Title:
Solution structure of oxidized human cytochrome c
Deposition date:
2015-11-24
Original release date:
2016-02-15
Authors:
Imai, Mizue; Saio, Tomohide; Kumeta, Hiroyuki; Uchida, Takeshi; Inagaki, Fuyuhiko; Ishimori, Koichiro
Citation:

Citation: Imai, Mizue; Saio, Tomohide; Kumeta, Hiroyuki; Uchida, Takeshi; Inagaki, Fuyuhiko; Ishimori, Koichiro. "Investigation of the redox-dependent modulation of structure and dynamics in human cytochrome c"  Biochem. Biophys. Res. Commun. 469, 978-984 (2016).
PubMed: 26718409

Assembly members:

Assembly members:
Cyt_c, polymer, 104 residues, 11640.677 Da.
HEME C, non-polymer, 618.503 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET21

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Cyt_c: GDVEKGKKIFIMKCSQCHTV EKGGKHKTGPNLHGLFGRKT GQAPGYSYTAANKNKGIIWG EDTLMEYLENPKKYIPGTKM IFVGIKKKEERADLIAYLKK ATNE

Data sets:
Data typeCount
13C chemical shifts465
15N chemical shifts105
1H chemical shifts774

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Cytochrome c1
2HEME C2

Entities:

Entity 1, Cytochrome c 104 residues - 11640.677 Da.

1   GLYASPVALGLULYSGLYLYSLYSILEPHE
2   ILEMETLYSCYSSERGLNCYSHISTHRVAL
3   GLULYSGLYGLYLYSHISLYSTHRGLYPRO
4   ASNLEUHISGLYLEUPHEGLYARGLYSTHR
5   GLYGLNALAPROGLYTYRSERTYRTHRALA
6   ALAASNLYSASNLYSGLYILEILETRPGLY
7   GLUASPTHRLEUMETGLUTYRLEUGLUASN
8   PROLYSLYSTYRILEPROGLYTHRLYSMET
9   ILEPHEVALGLYILELYSLYSLYSGLUGLU
10   ARGALAASPLEUILEALATYRLEULYSLYS
11   ALATHRASNGLU

Entity 2, HEME C - C34 H34 Fe N4 O4 - 618.503 Da.

1   HEC

Samples:

sample_1: Cyt c, [U-99% 13C; U-99% 15N], 0.5 – 1 mM; sodium phosphate 50 mM; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 50 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HN(CA)HAsample_1isotropicsample_conditions_1
3D HCCH-TOCSY aliphaticsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D HCCH-TOCSY aromaticsample_1isotropicsample_conditions_1
HbCbCgCdHdsample_1isotropicsample_conditions_1
HbCbCgCdCeHesample_1isotropicsample_conditions_1

Software:

VNMRJ, Varian - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TALOS+, Yang Shen,Frank Delaglio,Gabriel Cornilescu, Ad bax - data analysis

SPARKY, Goddard - chemical shift assignment, peak picking, refinement

CYANA, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

NMR spectrometers:

  • Agilent INOVA 800 MHz
  • Agilent INOVA 600 MHz
  • Agilent INOVA 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks