BMRB Entry 17884
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17884
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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
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 35 |
| 1H chemical shifts | 107 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | rat_beta_amyloid_1 | 1 |
| 2 | rat_beta_amyloid_2 | 1 |
| 3 | ZINC ION | 2 |
Entities:
Entity 1, rat_beta_amyloid_1 18 residues - 1860.979 Da.
| 1 | ACE | ASP | ALA | GLU | PHE | GLY | HIS | ASP | SER | GLY | ||||
| 2 | PHE | GLU | VAL | ARG | HIS | GLN | LYS | NH2 |
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D DQF-COSY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_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 |