BMRB Entry 36327

Name: Solution NMR structure of NF1; de novo designed protein with a novel fold
Published: 2022-05-24

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PDB ID: 7bpl
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36327
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution NMR structure of NF1; de novo designed protein with a novel fold PubMed: 37400653

Deposition date: 2020-03-23 Original release date: 2022-05-24

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

Citation: Minami, S.; Kobayashi, N.; 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, 110 residues, 12525.046 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: GDADKIMEQAKRQDPNAQVY KVTTPDEIEEAVRRIEKYGA QVVLIIYTSSGIVILVAVRD PSQADQILKEAKKQNPSATF VRLEGVSPDDLRRQVEDVWR GSLEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list

Data type	Count
13C chemical shifts	457
15N chemical shifts	104
1H chemical shifts	743

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_1 110 residues - 12525.046 Da.

1	GLY	ASP	ALA	ASP	LYS	ILE	MET	GLU	GLN	ALA
2	LYS	ARG	GLN	ASP	PRO	ASN	ALA	GLN	VAL	TYR
3	LYS	VAL	THR	THR	PRO	ASP	GLU	ILE	GLU	GLU
4	ALA	VAL	ARG	ARG	ILE	GLU	LYS	TYR	GLY	ALA
5	GLN	VAL	VAL	LEU	ILE	ILE	TYR	THR	SER	SER
6	GLY	ILE	VAL	ILE	LEU	VAL	ALA	VAL	ARG	ASP
7	PRO	SER	GLN	ALA	ASP	GLN	ILE	LEU	LYS	GLU
8	ALA	LYS	LYS	GLN	ASN	PRO	SER	ALA	THR	PHE
9	VAL	ARG	LEU	GLU	GLY	VAL	SER	PRO	ASP	ASP
10	LEU	ARG	ARG	GLN	VAL	GLU	ASP	VAL	TRP	ARG
11	GLY	SER	LEU	GLU	HIS	HIS	HIS	HIS	HIS	HIS

Samples:

sample_1: NF1, [U-100% 13C; U-100% 15N], 0.9 mM; potassium phosphate 1.1 mM; sodium chloride 50 mM; sodium phosphate 5.6 mM; H2O 95%; D2O, [U-2H], 5%

sample_2: NF1, [U-100% 13C; U-100% 15N], 0.2 mM; Pf1 phage 12 mg/mL; potassium phosphate 1.1 mM; sodium chloride 50 mM; sodium phosphate 5.6 mM; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 57 mM; pH: 7.4; 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 HNCO	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY aliphatic	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY aromatic	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 IPAP-HSQC	sample_1	isotropic	sample_conditions_1
2D IPAP-HSQC	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 v2.01.14, Kobayashi, N. - data analysis

MAGRO v2.01.29, Kobayashi, N. - peak picking

NMRPipe v2012, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

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

TopSpin v3.2, Bruker Biospin - collection

NMR spectrometers:

Bruker AVANCE III 800.1339 MHz
Bruker AVANCE III 950 MHz

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

1	GLY	ASP	ALA	ASP	LYS	ILE	MET	GLU	GLN	ALA
2	LYS	ARG	GLN	ASP	PRO	ASN	ALA	GLN	VAL	TYR
3	LYS	VAL	THR	THR	PRO	ASP	GLU	ILE	GLU	GLU
4	ALA	VAL	ARG	ARG	ILE	GLU	LYS	TYR	GLY	ALA
5	GLN	VAL	VAL	LEU	ILE	ILE	TYR	THR	SER	SER
6	GLY	ILE	VAL	ILE	LEU	VAL	ALA	VAL	ARG	ASP
7	PRO	SER	GLN	ALA	ASP	GLN	ILE	LEU	LYS	GLU
8	ALA	LYS	LYS	GLN	ASN	PRO	SER	ALA	THR	PHE
9	VAL	ARG	LEU	GLU	GLY	VAL	SER	PRO	ASP	ASP
10	LEU	ARG	ARG	GLN	VAL	GLU	ASP	VAL	TRP	ARG
11	GLY	SER	LEU	GLU	HIS	HIS	HIS	HIS	HIS	HIS

1	GLY	ASP	ALA	ASP	LYS	ILE	MET	GLU	GLN	ALA
2	LYS	ARG	GLN	ASP	PRO	ASN	ALA	GLN	VAL	TYR
3	LYS	VAL	THR	THR	PRO	ASP	GLU	ILE	GLU	GLU
4	ALA	VAL	ARG	ARG	ILE	GLU	LYS	TYR	GLY	ALA
5	GLN	VAL	VAL	LEU	ILE	ILE	TYR	THR	SER	SER
6	GLY	ILE	VAL	ILE	LEU	VAL	ALA	VAL	ARG	ASP
7	PRO	SER	GLN	ALA	ASP	GLN	ILE	LEU	LYS	GLU
8	ALA	LYS	LYS	GLN	ASN	PRO	SER	ALA	THR	PHE
9	VAL	ARG	LEU	GLU	GLY	VAL	SER	PRO	ASP	ASP
10	LEU	ARG	ARG	GLN	VAL	GLU	ASP	VAL	TRP	ARG
11	GLY	SER	LEU	GLU	HIS	HIS	HIS	HIS	HIS	HIS

1	GLY	ASP	ALA	ASP	LYS	ILE	MET	GLU	GLN	ALA
2	LYS	ARG	GLN	ASP	PRO	ASN	ALA	GLN	VAL	TYR
3	LYS	VAL	THR	THR	PRO	ASP	GLU	ILE	GLU	GLU
4	ALA	VAL	ARG	ARG	ILE	GLU	LYS	TYR	GLY	ALA
5	GLN	VAL	VAL	LEU	ILE	ILE	TYR	THR	SER	SER
6	GLY	ILE	VAL	ILE	LEU	VAL	ALA	VAL	ARG	ASP
7	PRO	SER	GLN	ALA	ASP	GLN	ILE	LEU	LYS	GLU
8	ALA	LYS	LYS	GLN	ASN	PRO	SER	ALA	THR	PHE
9	VAL	ARG	LEU	GLU	GLY	VAL	SER	PRO	ASP	ASP
10	LEU	ARG	ARG	GLN	VAL	GLU	ASP	VAL	TRP	ARG
11	GLY	SER	LEU	GLU	HIS	HIS	HIS	HIS	HIS	HIS