BMRB Entry 36331

Name: Solution NMR structure of NF6; de novo designed protein with a novel fold
Published: 2021-03-29

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PDB ID: 7bqb
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36331
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution NMR structure of NF6; de novo designed protein with a novel fold PubMed: 37400653

Deposition date: 2020-03-24 Original release date: 2021-03-29

Authors: Kobayashi, N.; Nagashima, T.; Minami, S.; Koga, R.; Chikenji, G.; Koga, N.

Citation: Minami, S.; Kobayashi, T.; Sugiki, T.; Nagashima, T.; Fujiwara, T.; Koga, R.; Chikenji, G.; Koga, N.. "Exploration of novel alpha-beta protein folds through de novo design" Nat. Struct. Mol. Biol. 30, 1132-1140 (2023).

Assembly members:
entity_1, polymer, 106 residues, 12499.396 Da.

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

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

Entity Sequences (FASTA):
entity_1: GKLYEVDSPDSVEKIARELG LSEEQLRRIQKEFERAERKG KLVIVYLTSDGKVEIREVTS EEELEKILKKLGVDEEIIRR IKRLRKEGQIKLVIIEGSLE HHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	448
15N chemical shifts	101
1H chemical shifts	738

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 106 residues - 12499.396 Da.

1

GLY

LYS

LEU

TYR

GLU

VAL

ASP

SER

PRO

ASP

2

SER

VAL

GLU

LYS

ILE

ALA

ARG

GLU

LEU

GLY

3

LEU

SER

GLU

GLN

LEU

ARG

ILE

GLN

4

LYS

GLU

PHE

GLU

ARG

ALA

GLU

ARG

LYS

GLY

5

LYS

LEU

VAL

ILE

VAL

TYR

LEU

THR

SER

ASP

6

GLY

LYS

VAL

GLU

ILE

ARG

GLU

VAL

THR

SER

7

GLU

LEU

GLU

LYS

ILE

LEU

LYS

8

LEU

GLY

VAL

ASP

GLU

ILE

ARG

9

ILE

LYS

ARG

LEU

ARG

LYS

GLU

GLY

GLN

ILE

10

LYS

LEU

VAL

ILE

GLU

GLY

SER

LEU

GLU

11

HIS

Samples:

sample_1: NF6, [U-100% 13C; U-100% 15N], 0.7 mM; potassium phosphate 7.4 mM; sodium chloride 50 mM; sodium phosphate 1.1 mM; H2O 95%; D2O, [U-2H], 5%

sample_2: NF6, [U-100% 13C; U-100% 15N], 0.2 mM; Pf1 phage 8 mg/mL; potassium phosphate 7.4 mM; sodium chloride 50 mM; sodium phosphate 1.1 mM; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 58.5 mM; pH: 6.0; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D BEST-HNCO	sample_1	isotropic	sample_conditions_1
3D BEST-HNCACB	sample_1	isotropic	sample_conditions_1
3D BEST-HN(CO)CACB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY aliphatic	sample_1	isotropic	sample_conditions_1
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
2D 1H-15N HSQC IPAP	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC IPAP	sample_2	anisotropic	sample_conditions_1

Software:

Amber v12, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA v3.98, Guntert, Mumenthaler and Wuthrich - chemical shift assignment, structure calculation

MAGRO v2.01.38, Kobayashi, N. - peak picking

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

NMRView v9.0, Johnson, One Moon Scientific - data analysis

TALOS v2017, Cornilescu, Delaglio and Bax - data analysis

TopSpin v3.2, Bruker Biospin - collection

qMDD v2.6, Orekhov, V. Jaravine, M. Mayzel, K. Kazimierczuk - processing

NMR spectrometers:

Bruker AVANCE III 600 MHz
Bruker AVANCE III 700 MHz
Bruker AVANCE III 900 MHz

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