BMRB Entry 36337

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PDB ID:
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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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:
Data typeCount
13C chemical shifts538
15N chemical shifts129
1H chemical shifts889

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 130 residues - 15296.273 Da.

1   GLYASPGLUARGLYSLEUGLUGLUVALTHR
2   GLUGLUMETARGLYSMETALAGLUASNMET
3   ASPGLYGLNASPPROGLULYSVALLYSGLU
4   ILEVALARGARGALALEUGLNGLNMETALA
5   ASNASPASNPROGLUVALSERGLUGLNLEU
6   ARGGLULEUALALYSARGLYSGLYTHRSER
7   PROSERGLUVALILELYSASPLEUALAGLU
8   GLNVALTRPARGALAMETGLUARGALAARG
9   GLUGLYASPLYSASPTHRALAARGGLULEU
10   ILEARGLYSPHEALAASPASPLEUGLYILE
11   SERPROGLUGLNVALLYSLYSPHEILELYS
12   ILEMETARGGLUVALGLNARGLYSGLUASP
13   GLYSERLEUGLUHISHISHISHISHISHIS

Samples:

sample_1: Gogy, [U-100% 13C; U-100% 15N], 0.9 mM; potassium phosphate 6.8 mM; sodium chloride 50 mM; sodium phosphate 3.20 mM; H2O 95%; D2O, [U-2H], 5%

sample_2: Gogy, [U-100% 13C; U-100% 15N], 0.2 mM; Pf1 phage 7 mg/mL; potassium phosphate 6.8 mM; sodium chloride 50 mM; sodium phosphate 3.2 mM; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 60 mM; pH: 6.52; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D BEST-HNCOsample_1isotropicsample_conditions_1
3D BEST-HNCACBsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HCCH-TOCSY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D 1H-15N HSQC IPAPsample_1isotropicsample_conditions_1
2D 1H-15N HSQC IPAPsample_2anisotropicsample_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, 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