BMRB Entry 25551

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25551
MolProbity Validation Chart

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Title:
Backbone amide chemical shift assignments of the CN-bound yeast cytochrome c peroxidase covalently cross-linked to yeast iso-1 cytochrome c
Deposition date:
2015-03-24
Original release date:
2015-05-08
Authors:
Volkov, Alexander; Van de Water, Karen
Citation:

Citation: Van de Water, Karen; Sterckx, Yann; Volkov, Alexander. "The low-affinity complex of cytochrome c and its peroxidase"  Nat. Commun. 6, 7073-7073 (2015).
PubMed: 25944250

Assembly members:

Assembly members:
CcP, polymer, 294 residues, 33543.504 Da.
Cc, polymer, 108 residues, 12073.930 Da.
Cc1, polymer, 108 residues, 12073.931 Da.
PROTOPORPHYRIN IX CONTAINING FE, non-polymer, 616.487 Da.
HEME C, non-polymer, 618.503 Da.

Natural source:

Natural source:   Common Name: baker's yeast   Taxonomy ID: 4932   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET24

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CcP: TTPLVHVASVEKGRSYEDFQ KVYNAIALKLREDDEYDNYI GYGPVLVRLAWHTSGTWDKH DNTGGSYGGTYRFKKEFNDP SNAGLQNGFKFLEPIHKEFP WISSGDLFSLGGVTAVQEMQ GPKIPWRAGRVDTPEDTTPD NGRLPDADKDADYVRTFFQR LNMNDREVVALMGAHALGKT HLKNSGYEGPWGAANNCFTN EFYLNLLNEDWKLEKNDANN EQWDSKSGYMMLPTDYSLIQ DPKYLSIVKEYANDQDKFFK DFSKAFEKLLENGITFPKDA PSPFIFKTLEEQGL
Cc: AEFKAGSAKKGATLFKTRCL QCHTVEKGGPHKVGPNLHGI FGRHSGQAEGYSYTDANIKK NVLWDENNMSEYLTNPKKYI PGTKMCFGGLKKEKDRNDLI TYLKKATE
Cc1: TEFKAGSAKKGATLFKTRCL QCHTVEKGGPHKVGPNLHGI FGRHSGQAEGYSYTDANIKK NVLWDENNMSEYLTNPKKYI PGTKMAFGGLKKEKDRNDLI TYLKKACE

Data sets:
Data typeCount
15N chemical shifts229
1H chemical shifts229

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22
3entity_33
4HEM4
5HEC_15
6HEC_25

Entities:

Entity 1, entity_1 294 residues - 33543.504 Da.

1   THRTHRPROLEUVALHISVALALASERVAL
2   GLULYSGLYARGSERTYRGLUASPPHEGLN
3   LYSVALTYRASNALAILEALALEULYSLEU
4   ARGGLUASPASPGLUTYRASPASNTYRILE
5   GLYTYRGLYPROVALLEUVALARGLEUALA
6   TRPHISTHRSERGLYTHRTRPASPLYSHIS
7   ASPASNTHRGLYGLYSERTYRGLYGLYTHR
8   TYRARGPHELYSLYSGLUPHEASNASPPRO
9   SERASNALAGLYLEUGLNASNGLYPHELYS
10   PHELEUGLUPROILEHISLYSGLUPHEPRO
11   TRPILESERSERGLYASPLEUPHESERLEU
12   GLYGLYVALTHRALAVALGLNGLUMETGLN
13   GLYPROLYSILEPROTRPARGALAGLYARG
14   VALASPTHRPROGLUASPTHRTHRPROASP
15   ASNGLYARGLEUPROASPALAASPLYSASP
16   ALAASPTYRVALARGTHRPHEPHEGLNARG
17   LEUASNMETASNASPARGGLUVALVALALA
18   LEUMETGLYALAHISALALEUGLYLYSTHR
19   HISLEULYSASNSERGLYTYRGLUGLYPRO
20   TRPGLYALAALAASNASNCYSPHETHRASN
21   GLUPHETYRLEUASNLEULEUASNGLUASP
22   TRPLYSLEUGLULYSASNASPALAASNASN
23   GLUGLNTRPASPSERLYSSERGLYTYRMET
24   METLEUPROTHRASPTYRSERLEUILEGLN
25   ASPPROLYSTYRLEUSERILEVALLYSGLU
26   TYRALAASNASPGLNASPLYSPHEPHELYS
27   ASPPHESERLYSALAPHEGLULYSLEULEU
28   GLUASNGLYILETHRPHEPROLYSASPALA
29   PROSERPROPHEILEPHELYSTHRLEUGLU
30   GLUGLNGLYLEU

Entity 2, entity_2 108 residues - 12073.930 Da.

1   ALAGLUPHELYSALAGLYSERALALYSLYS
2   GLYALATHRLEUPHELYSTHRARGCYSLEU
3   GLNCYSHISTHRVALGLULYSGLYGLYPRO
4   HISLYSVALGLYPROASNLEUHISGLYILE
5   PHEGLYARGHISSERGLYGLNALAGLUGLY
6   TYRSERTYRTHRASPALAASNILELYSLYS
7   ASNVALLEUTRPASPGLUASNASNMETSER
8   GLUTYRLEUTHRASNPROLYSLYSTYRILE
9   PROGLYTHRLYSMETCYSPHEGLYGLYLEU
10   LYSLYSGLULYSASPARGASNASPLEUILE
11   THRTYRLEULYSLYSALATHRGLU

Entity 3, entity_3 108 residues - 12073.931 Da.

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

Entity 4, HEM - C34 H32 Fe N4 O4 - 616.487 Da.

1   HEM

Entity 5, HEC_1 - C34 H34 Fe N4 O4 - 618.503 Da.

1   HEC

Samples:

sample_1: CcP, [U-2H; U-15N], 0.4 mM; Cc 0.4 mM; Cc1 0.4 mM; sodium phosphate 20 mM; H2O 93%; D2O, [U-2H], 7%

sample_conditions_1: ionic strength: 15 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1

Software:

VNMRJ, Varian - collection

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

CcpNMR, CCPN - chemical shift assignment, data analysis, peak picking

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMR spectrometers:

  • Varian Uniform NMR System 800 MHz

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