BMRB Entry 36336

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

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PDB ID: 7bqn
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36336
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-C Rei; 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, 121 residues, 14110.003 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: GDEAEKQAERALELVRKSPD LLKKLLEAMAEELKRQGKSP DEIQKAKDEVKTKVEQAIRE WKQGNEEQARKDMRKVLKSP AFKQAVKVMEEQEPNNPEVQ ELKKAMEEAERGSLEHHHHH H

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	488
15N chemical shifts	121
1H chemical shifts	775

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_1 121 residues - 14110.003 Da.

1

GLY

ASP

GLU

ALA

GLU

LYS

GLN

ALA

GLU

ARG

2

ALA

LEU

GLU

LEU

VAL

ARG

LYS

SER

PRO

ASP

3

LEU

LYS

LEU

GLU

ALA

MET

ALA

4

GLU

LEU

LYS

ARG

GLN

GLY

LYS

SER

PRO

5

ASP

GLU

ILE

GLN

LYS

ALA

LYS

ASP

GLU

VAL

6

LYS

THR

LYS

VAL

GLU

GLN

ALA

ILE

ARG

GLU

7

TRP

LYS

GLN

GLY

ASN

GLU

GLN

ALA

ARG

8

LYS

ASP

MET

ARG

LYS

VAL

LEU

LYS

SER

PRO

9

ALA

PHE

LYS

GLN

ALA

VAL

LYS

VAL

MET

GLU

10

GLU

GLN

GLU

PRO

ASN

PRO

GLU

VAL

GLN

11

GLU

LEU

LYS

ALA

MET

GLU

ALA

GLU

12

ARG

GLY

SER

LEU

GLU

HIS

13

HIS

Samples:

sample_1: Rei, [U-100% 13C; U-100% 15N], 0.9 mM; potassium phosphate 4.5 mM; sodium chloride 50 mM; sodium phosphate 5.5 mM; H2O 95%; D2O, [U-2H], 5%

sample_2: Rei, [U-100% 13C; U-100% 15N], 0.2 mM; Pf1 phage 7 mg/mL; potassium phosphate 4.5 mM; sodium chloride 50 mM; sodium phosphate 5.5 mM; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 56.6 mM; pH: 6.89; 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 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC IPAP	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_2	isotropic	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 v2.01.24, Updated version of Kujira (Kobayashi, N. et al., 2007) - 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

NMR spectrometers:

Bruker AVANCE III 600 MHz
Bruker AVANCE III 800 MHz
Bruker AVANCE III 950 MHz

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