BMRB Entry 25660

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25660
MolProbity Validation Chart

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Title:
NMR structure of the Y48pCMF variant of human cytochrome c in its reduced state
Deposition date:
2015-06-15
Original release date:
2016-12-08
Authors:
Moreno-Beltran, Blas; Del Conte, Rebecca; Diaz-Quintana, Antonio; De la Rosa, Miguel; Turano, Paola; Diaz-Moreno, Irene
Citation:

Citation: Diaz-Moreno, Irene. "NMR structure of the Y48pCMF variant of human cytochrome c in its reduced state"  Nat. Struct. Biol. ., .-..

Assembly members:

Assembly members:
entity, polymer, 104 residues, 12504.514 Da.
PROTOPORPHYRIN IX CONTAINING FE, non-polymer, 616.487 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: pCcY48AMBER

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GDVEKGKKIFIMKCSQCHTV EKGGKHKTGPNLHGLFGRKT GQAPGYSXTAANKNKGIIWG EDTLMEYLENPKKYIPGTKM IFVGIKKKEERADLIAYLKK ATNE

Data sets:
Data typeCount
13C chemical shifts423
15N chemical shifts95
1H chemical shifts745

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity1
2PROTOPORPHYRIN IX CONTAINING FE2

Entities:

Entity 1, entity 104 residues - 12504.514 Da.

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

Entity 2, PROTOPORPHYRIN IX CONTAINING FE - C34 H32 Fe N4 O4 - 616.487 Da.

1   HEM

Samples:

sample_1: entity, [U-99% 13C; U-99% 15N], 0.7 mM; P-CARBOXI-METHYL-L-PHENYLALANINE 0.7 mM; PROTOPORPHYRIN IX CONTAINING FE 0.7 mM; phosphate buffer 10 mM; H2O 90%; D2O 10%

sample_2: entity, [U-99% 15N], 0.7 mM; P-CARBOXI-METHYL-L-PHENYLALANINE 0.7 mM; PROTOPORPHYRIN IX CONTAINING FE 0.7 mM; phosphate buffer 10 mM; H2O 90%; D2O 10%

sample_3: entity 0.6 mM; P-CARBOXI-METHYL-L-PHENYLALANINE 0.6 mM; PROTOPORPHYRIN IX CONTAINING FE 0.6 mM; phosphate buffer 10 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.05 M; pH: 6.3; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_3isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_3isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

TOPSPIN, Bruker Biospin - collection, processing

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

CARA, Keller and Wuthrich - chemical shift assignment, chemical shift calculation, data analysis, peak picking

XEASY, Bartels et al. - chemical shift assignment, chemical shift calculation, data analysis, peak picking, processing

NMR spectrometers:

  • Bruker Avance 950 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 500 MHz
  • Bruker Avance 500 MHz

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