BMRB Entry 36337

Name: Solution NMR structure of fold-Z Gogy; de novo designed protein with an asymmetric all-alpha topology
Published: 2022-01-28

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PDB ID: 7bqq
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36337
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:

Solution NMR structure of fold-Z Gogy; de novo designed protein with an asymmetric all-alpha topology

Deposition date:

2020-03-25

Original release date:

2022-01-28

Authors:

Kobayashi, N.; Sugiki, T.; Fujiwara, T.; Sakuma, K.; Kosugi, T.; Koga, R.; Koga, N.

Citation:

Citation: Sakuma, Koya; Kobayashi, Naohiro; Sugiki, Toshihiko; Nagashima, Toshio; Fujiwara, Toshimichi; Suzuki, Kano; Kobayashi, Naoya; Murata, Takeshi; Kosugi, Takahiro; Tatsumi-Koga, Rie; Koga, Nobuyasu. "Design of complicated all-alpha protein structures" Nat. Struct. Mol. Biol. 31, 275-282 (2024).
PubMed: 38177681

Assembly members:

Assembly members:
entity_1, polymer, 130 residues, 15296.273 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GDERKLEEVTEEMRKMAENM DGQDPEKVKEIVRRALQQMA NDNPEVSEQLRELAKRKGTS PSEVIKDLAEQVWRAMERAR EGDKDTARELIRKFADDLGI SPEQVKKFIKIMREVQRKED GSLEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	538
15N chemical shifts	129
1H chemical shifts	889

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_1 130 residues - 15296.273 Da.

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

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 1H-13C NOESY aliphatic	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 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

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

BMRB Entry 36337

Additional metadata:

Assembly:

Entities:

Samples:

Experiments:

Software:

NMR spectrometers:

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

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

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