BMRB Entry 19602

Name: Zinc induced dimer of the metal binding domain 1-16 of human amyloid beta-peptide with Alzheimer`s disease pathogenic English mutation H6R
Published: 2014-11-10

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PDB ID: 2mgt
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19602
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Zinc induced dimer of the metal binding domain 1-16 of human amyloid beta-peptide with Alzheimer`s disease pathogenic English mutation H6R

Deposition date:

2013-11-06

Original release date:

2014-11-10

Authors:

Polshakov, Vladimir; Istrate, Andrey; Kozin, Sergey

Citation:

Citation: Istrate, Andrey; Makarov, Alexander; Kozin, Sergey; Polshakov, Vladimir. "Optimization of the methods for small peptide solution structure determination by NMR spectroscopy" Mol. Biol. (Mosk) 44, 1075-1085 (2010).
PubMed: 21290829

Assembly members:

Assembly members:
entity_1, polymer, 18 residues, 1977.121 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: XDAEFRRDSGYEVHHQKX

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	157
15N chemical shifts	38
1H chemical shifts	331

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Human-amyloid-peptide_1	1
2	Human-amyloid-peptide_2	1
3	ZINC ION	2

Entities:

Entity 1, Human-amyloid-peptide_1 18 residues - 1977.121 Da.

1

ACE

ASP

ALA

GLU

PHE

ARG

ASP

SER

GLY

2

TYR

GLU

VAL

HIS

GLN

LYS

NH2

Entity 2, ZINC ION - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: entity_1 2 mM; bis-Tris, [U-99% 2H], 20 mM; TSP, d4 (100%), 40 uM; H2O 90%; D2O 10%

sample_2: entity_1 2 mM; bis-Tris, [U-99% 2H], 20 mM; TSP, d4 (100%), 40 uM; D2O 100%

sample_3: entity_1 2 mM; zinc cloride 1 mM; bis-Tris, [U-99% 2H], 20 mM; TSP, d4 (100%), 40 uM; H2O 90%; D2O 10%

sample_4: entity_1 2 mM; zinc cloride 1 mM; bis-Tris, [U-99% 2H], 20 mM; TSP, d4 (100%), 40 uM; D2O 100%

sample_conditions_1: pH: 6.8; pressure: 1 atm; temperature: 274 K

sample_conditions_2: pD: 7.2; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_4	isotropic	sample_conditions_2

Software:

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

TOPSPIN, Bruker Biospin - collection

SPARKY, Goddard - chemical shift assignment

NMRest, Polshakov V. I. - data analysis

GROMACS v4.5.4, Van Der Spoel, Lindahl Hess, Groenhof, Mark and Berendsen - refinement

CPMD, CPMD consortium - geometry optimization

PyMol, DeLano - data analysis

InsightII, Accelrys Software Inc. - data analysis

ProcheckNMR, Laskowski and MacArthur - data analysis

NMR spectrometers:

Bruker Avance 600 MHz