BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 17806

Title: NMR structure of the calcium-bound form of the protein YP_001302112.1 from Parabacteroides distasonis

Deposition date: 2011-07-25 Original release date: 2011-08-26

Authors: Serrano, Pedro; Geralt, Michael; Mohanty, Biswaranjan; Wuthrich, Kurt

Citation: Serrano, Pedro; Geralt, Michael; Mohanty, Biswaranjan; Wuthrich, Kurt. "NMR structure of the calcium-bound form of the protein YP_001302112.1 from Parabacteroides distasonis"  .

Assembly members:
entity, polymer, 129 residues, 13807.372 Da.
CA, non-polymer, 40.078 Da.

Natural source:   Common Name: Parabacteroides distasonis   Taxonomy ID: 823   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Parabacteroides distasonis

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

Entity Sequences (FASTA):
entity: KDDDEPGGKGAMYEVTIEQS GDFRSFIKSVVVVANGTQLK DGATGESLASPVILSDEELA VEKVTLSTTGKAIEFAVSGG VVDGEDGVVNEPMQWVVTVY KNGKEIEKKSLVFRDGKEIS TDDLNLYYN

Data sets:
Data typeCount
13C chemical shifts532
15N chemical shifts134
1H chemical shifts852

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1YP_001302112.11
2Calcium ions2

Entities:

Entity 1, YP_001302112.1 129 residues - 13807.372 Da.

1   LYSASPASPASPGLUPROGLYGLYLYSGLY
2   ALAMETTYRGLUVALTHRILEGLUGLNSER
3   GLYASPPHEARGSERPHEILELYSSERVAL
4   VALVALVALALAASNGLYTHRGLNLEULYS
5   ASPGLYALATHRGLYGLUSERLEUALASER
6   PROVALILELEUSERASPGLUGLULEUALA
7   VALGLULYSVALTHRLEUSERTHRTHRGLY
8   LYSALAILEGLUPHEALAVALSERGLYGLY
9   VALVALASPGLYGLUASPGLYVALVALASN
10   GLUPROMETGLNTRPVALVALTHRVALTYR
11   LYSASNGLYLYSGLUILEGLULYSLYSSER
12   LEUVALPHEARGASPGLYLYSGLUILESER
13   THRASPASPLEUASNLEUTYRTYRASN

Entity 2, Calcium ions - Ca - 40.078 Da.

1   CA

Samples:

sample_1: YP_001302112.1, [U-98% 13C; U-98% 15N], 1.2 mM; calcium chloride 10 mM; sodium chloride 25 mM; sodium phosphate 20 mM; sodium azide 5 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 0.145 M; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
5D APSY CBCACONHsample_1isotropicsample_conditions_1
4D APSY HACANHsample_1isotropicsample_conditions_1
5D APSY HACACONHsample_1isotropicsample_conditions_1

Software:

CYANA, G ntert P. - refinement

Opalp, Luginbuhl, Guntert, Billeter and Wuthrich - refinement

TOPSPIN, Bruker Biospin - collection, data analysis, processing

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

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

BMRB 17799
PDB
EMBL CUP04873 CUP86285 CUQ25107
GB AAO45318 ABR42490 EFG18115 EFK63750 EIY16653
REF NP_818973 WP_005842168 WP_007659490 WP_032583709

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