BMRB Entry 19970

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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/BMR19970
MolProbity Validation Chart

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Title:
NMR structure of NKR-5-3B
Deposition date:
2014-05-13
Original release date:
2015-05-11
Authors:
Rosengren, K. Johan; Craik, David
Citation:

Citation: Himeno, Kohei; Rosengren, K. Johan; Inoue, Tomoko; Perez, Rodney; Colgrave, Michelle; Lee, Han Siean; Fujita, Koji; Ishibashi, Naoki; Zendo, Takeshi; Wilaipun, Pongtep; Nakayama, Jiro; Leelawatcharamas, Vichien; Jikuya, Hiroyuki; Craik, David; Sonomoto, Kenji. "Identification, Characterization, and Three-Dimensional Structure of the Novel Circular Bacteriocin, Enterocin NKR-5-3B, from Enterococcus faecium"  J. Biol. Chem. ., .-..

Assembly members:

Assembly members:
NKR-5-3B, polymer, 64 residues, 6340.563 Da.

Natural source:

Natural source:   Common Name: firmicutes   Taxonomy ID: 1351   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Enterococcus faecalis

Experimental source:

Experimental source:   Production method: purified from the natural source

Entity Sequences (FASTA):

Entity Sequences (FASTA):
NKR-5-3B: LTANLGISSYAAKKVIDIIN TGSAVATIIALVTAVVGGGL ITAGIVATAKSLIKKYGAKY AAAW

Data sets:
Data typeCount
13C chemical shifts154
15N chemical shifts62
1H chemical shifts315

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1Enterocin NKR-5-3B1

Entities:

Entity 1, Enterocin NKR-5-3B 64 residues - 6340.563 Da.

The N and C termini are linked by an amide bond.

1   LEUTHRALAASNLEUGLYILESERSERTYR
2   ALAALALYSLYSVALILEASPILEILEASN
3   THRGLYSERALAVALALATHRILEILEALA
4   LEUVALTHRALAVALVALGLYGLYGLYLEU
5   ILETHRALAGLYILEVALALATHRALALYS
6   SERLEUILELYSLYSTYRGLYALALYSTYR
7   ALAALAALATRP

Samples:

sample_1: NKR-5-3B 6 mg/mL; H2O 90%; D2O 10%

sample_2: NKR-5-3B 6 mg/mL; D2O 100%

sample_conditions_1: ionic strength: 0 M; pH: 5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - collection, processing

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

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

  • Bruker Avance II 900 MHz
  • Bruker Avance 600 MHz

Related Database Links:

PDB
DBJ BAT21392

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