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 17884

Title: METAL BINDING DOMAIN OF RAT BETA-AMYLOID   PubMed: 22225807

Deposition date: 2011-08-25 Original release date: 2011-10-24

Authors: Polshakov, Vladimir; Istrate, Andrey; Kozin, Sergey; Makarov, Alexander

Citation: Istrate, Andrey; Tsvetkov, Philipp; Mantsyzov, Alexey; Kulikova, Alexandra; Kozin, Sergey; Makarov, Alexander; Polshakov, Vladimir. "NMR solution structure of rat a(1-16): toward understanding the mechanism of rats' resistance to Alzheimer's disease."  Biophys. J. 102, 136-143 (2012).

Assembly members:
rat_beta_amyloid, polymer, 18 residues, 1860.979 Da.
ZN, non-polymer, 65.409 Da.

Natural source:   Common Name: Rat   Taxonomy ID: 10116   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Rattus norvegicus

Experimental source:   Production method: obtained from a vendor

Entity Sequences (FASTA):
rat_beta_amyloid: XDAEFGHDSGFEVRHQKX

Data sets:
Data typeCount
13C chemical shifts35
1H chemical shifts107

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1rat_beta_amyloid_11
2rat_beta_amyloid_21
3ZINC ION2

Entities:

Entity 1, rat_beta_amyloid_1 18 residues - 1860.979 Da.

1   ACEASPALAGLUPHEGLYHISASPSERGLY
2   PHEGLUVALARGHISGLNLYSNH2

Entity 2, ZINC ION - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: rat_beta_amyloid 5 mM; Zinc cloride 8 mM; TRIS, [U-100% 2H], 20 mM; sodium azide 0.1%; H2O 90%; D2O 10%

sample_2: rat_beta_amyloid 5 mM; Zinc cloride 8 mM; TRIS, [U-100% 2H], 20 mM; sodium azide 0.1%; D2O 100%

sample_conditions_1: ionic strength: 10 mM; pH: 7.1; pressure: 1 atm; temperature: 278 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

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

SPARKY, Goddard - data analysis

AngleSearch, V. Polshakov - data analysis

GROMACS v3.3.1, Van Der Spoel et al. - structure solution

GROMACS_CPMD, Biswas & Gogonea - geometry optimization

ProcheckNMR, Laskowski and MacArthur - data analysis

InsightII, Accelrys Software Inc. - data analysis

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

PDB
DBJ BAC34997 BAC36369 BAE27986 BAE34927 BAE35313
EMBL CAA30488
GB AAA37139 AAB40919 AAB41502 AAB86608 AAH05490
REF NP_001185752 NP_001185753 NP_001185754 NP_001185755 NP_031497
SP P08592 P12023