BMRB Entry 34064

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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/BMR34064
MolProbity Validation Chart

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Title:
Solution structure and dynamics of the first outer membrane cytochrome from Geobacter sulfurreducens
Deposition date:
2016-11-10
Original release date:
2017-04-06
Authors:
Dantas, J.; Silva, M.; Morgado, L.; Pantoja-Uceda, D.; Turner, D.; Bruix, M.; Salgueiro, C.
Citation:

Citation: Dantas, Joana; Silva, Marta; Pantoja-Uceda, David; Turner, David; Bruix, Marta; Salgueiro, Carlos. "Solution structure and dynamics of the outer membrane cytochrome OmcF from Geobacter sulfurreducens."  Biochim. Biophys. Acta 1858, 733-741 (2017).
PubMed: 28377068

Assembly members:

Assembly members:
entity_1, polymer, 80 residues, 8324.456 Da.
entity_HEC, non-polymer, 618.503 Da.

Natural source:

Natural source:   Common Name: Geobacter sulfurreducens   Taxonomy ID: 243231   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Geobacter sulfurreducens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli DH5[alpha]

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: AGGGELFATHCAGCHPQGGN TVHPEKTLARARREANGIRT VRDVAAYIRNPGPGMPAFGE AMIPPADALKIGEYVVASFP

Data sets:
Data typeCount
15N chemical shifts73
1H chemical shifts519

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_11
2HEME C2

Entities:

Entity 1, entity_1 80 residues - 8324.456 Da.

1   ALAGLYGLYGLYGLULEUPHEALATHRHIS
2   CYSALAGLYCYSHISPROGLNGLYGLYASN
3   THRVALHISPROGLULYSTHRLEUALAARG
4   ALAARGARGGLUALAASNGLYILEARGTHR
5   VALARGASPVALALAALATYRILEARGASN
6   PROGLYPROGLYMETPROALAPHEGLYGLU
7   ALAMETILEPROPROALAASPALALEULYS
8   ILEGLYGLUTYRVALVALALASERPHEPRO

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

1   HEC

Samples:

sample_2: Outer membrane protein, OmcF 2 mM

sample_3: Outer membrane protein, OmcF 2 mM

sample_1: Outer membrane protein, OmcF, [U-13C; U-15N], 2 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_3isotropicsample_conditions_3
2D 1H-1H COSYsample_3isotropicsample_conditions_3
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D 1H-1H TOCSYsample_2isotropicsample_conditions_2
2D 1H-1H COSYsample_2isotropicsample_conditions_2
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_3

Software:

DYANA, Guntert P., Guntert, Braun and Wuthrich - refinement, structure calculation

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz

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