BMRB Entry 36338

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

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PDB ID: 7bqr
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36338
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-K Mussoc; de novo designed protein with an asymmetric all-alpha topology

Deposition date:

2020-03-25

Original release date:

2022-01-28

Authors:

Kobayashi, N.; Nagashima, 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, 137 residues, 15536.427 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: GDEDKEKLKREAERALSEAL SEFEKQGKITPETLKRLAEE IAEAALAQQQGDSERLEKAA RRFAETLLRALKESGASAEE IEEAIERIRKALSKAPSPQL QKLANSPQWQTALQEAIKKA RQEKKEKGSLEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	513
15N chemical shifts	123
1H chemical shifts	792

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_1 137 residues - 15536.427 Da.

1

GLY

ASP

GLU

ASP

LYS

GLU

LYS

LEU

LYS

ARG

2

GLU

ALA

GLU

ARG

ALA

LEU

SER

GLU

ALA

LEU

3

SER

GLU

PHE

GLU

LYS

GLN

GLY

LYS

ILE

THR

4

PRO

GLU

THR

LEU

LYS

ARG

LEU

ALA

GLU

5

ILE

ALA

GLU

ALA

LEU

ALA

GLN

6

GLY

ASP

SER

GLU

ARG

LEU

GLU

LYS

ALA

7

ARG

PHE

ALA

GLU

THR

LEU

ARG

ALA

8

LEU

LYS

GLU

SER

GLY

ALA

SER

ALA

GLU

9

ILE

GLU

ALA

ILE

GLU

ARG

ILE

ARG

LYS

10

ALA

LEU

SER

LYS

ALA

PRO

SER

PRO

GLN

LEU

11

GLN

LYS

LEU

ALA

ASN

SER

PRO

GLN

TRP

GLN

12

THR

ALA

LEU

GLN

GLU

ALA

ILE

LYS

ALA

13

ARG

GLN

GLU

LYS

GLU

LYS

GLY

SER

LEU

14

GLU

HIS

Samples:

sample_1: foldK4, [U-100% 13C; U-100% 15N], 0.5 mM; potassium phosphate 1.06 mM; sodium chloride 155.2 mM; sodium phosphate 2.97 mM; H2O 95%; D2O, [U-2H], 5%

sample_2: foldK4, [U-100% 13C; U-100% 15N], 0.2 mM; Pf1 phage 10.0 mg/mL; potassium phosphate 1.06 mM; sodium chloride 155.2 mM; sodium phosphate 2.97 mM; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 160 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 HCACO	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(NCA)NH	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 H(CCO)NH	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
3D 1H-13C NOESY aliphatic	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 v2.01.34, Kobayashi, N. - peak picking

NMRPipe v2017, 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 peaks
SPARKY: Backbone or all simulated peaks