BMRB Entry 31017

Name: NMR solution structure of the De novo designed small beta-barrel protein 29_bp_sh3
Published: 2023-03-14

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PDB ID: 7uwy
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31017
MolProbity Validation Chart

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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:

NMR solution structure of the De novo designed small beta-barrel protein 29_bp_sh3

Deposition date:

2022-05-04

Original release date:

2023-03-14

Authors:

Peterson, F.; Kim, D.; Jensen, D.; Saleem, A.; Chow, C.; Volkman, B.; Baker, D.

Citation:

Citation: Kim, D.; Jensen, D.; Feldman, D.; Tischer, D.; Saleem, A.; Chow, C.; Li, X.; Carter, L.; Milles, L.; Nguyen, H.; Kang, A.; Bera, A.; Peterson, F.; Volkman, B.; Ovchinnikov, S.; Baker, D.. "De novo design of small beta barrel proteins" Proc. Natl. Acad. Sci. U. S. A. 120, e2207974120-e2207974120 (2023).
PubMed: 36897987

Assembly members:

Assembly members:
entity_1, polymer, 61 residues, 6886.716 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3) Vector: pET29

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SEVETVLRKAAERNKTVDIH TKSGTTVRVNVKRVDSKSVK VERNGQDLEISLDQITHVDG W

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	263
15N chemical shifts	65
1H chemical shifts	432

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 61 residues - 6886.716 Da.

1

SER

GLU

VAL

GLU

THR

VAL

LEU

ARG

LYS

ALA

2

ALA

GLU

ARG

ASN

LYS

THR

VAL

ASP

ILE

HIS

3

THR

LYS

SER

GLY

THR

VAL

ARG

VAL

ASN

4

VAL

LYS

ARG

VAL

ASP

SER

LYS

SER

VAL

LYS

5

VAL

GLU

ARG

ASN

GLY

GLN

ASP

LEU

GLU

ILE

6

SER

LEU

ASP

GLN

ILE

THR

HIS

VAL

ASP

GLY

7

TRP

Samples:

sample_1: 29_bp_sh3, [U-13C; U-15N], 1.25 mM; sodium phosphate 50 mM; sodium chloride 50 mM; sodium azide 0.02 % w/v

sample_conditions_1: ionic strength: 132 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1

Software:

TopSpin v3.6, Bruker Biospin - collection

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

XEASY, Bartels et al. - data analysis

GARANT, Bartels, Guntert, Billeter and Wuthrich - chemical shift assignment

CYANA v3.98.13, Guntert, Mumenthaler and Wuthrich - refinement, structure calculation

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization, refinement

TALOS, Cornilescu, Delaglio and Bax - data analysis

NMR spectrometers:

Bruker AVANCE III HD 600 MHz

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