BMRB

Biological Magnetic Resonance Data Bank


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BMRB Entry 36339

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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/BMR36339
MolProbity Validation Chart

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Title: Solution NMR structure of fold-U Nomur; de novo designed protein with an asymmetric all-alpha topology   PubMed: 38177681

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: 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).

Assembly members:
entity_1, polymer, 122 residues, 13466.042 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: GETKAKAAQEALRAAREQAT TPEAQKALEELEKVLKTASP EQWRQAAEKIFEAFREASNG NTEKAKKLLEEAARTAGASP EIIKKLASALERLAEEGAAK EAARQAEEVRKRGSLEHHHH HH

Data sets:
Data typeCount
13C chemical shifts484
15N chemical shifts119
1H chemical shifts738

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 122 residues - 13466.042 Da.

1   GLYGLUTHRLYSALALYSALAALAGLNGLU
2   ALALEUARGALAALAARGGLUGLNALATHR
3   THRPROGLUALAGLNLYSALALEUGLUGLU
4   LEUGLULYSVALLEULYSTHRALASERPRO
5   GLUGLNTRPARGGLNALAALAGLULYSILE
6   PHEGLUALAPHEARGGLUALASERASNGLY
7   ASNTHRGLULYSALALYSLYSLEULEUGLU
8   GLUALAALAARGTHRALAGLYALASERPRO
9   GLUILEILELYSLYSLEUALASERALALEU
10   GLUARGLEUALAGLUGLUGLYALAALALYS
11   GLUALAALAARGGLNALAGLUGLUVALARG
12   LYSARGGLYSERLEUGLUHISHISHISHIS
13   HISHIS

Samples:

sample_1: foldU5, [U-100% 13C; U-100% 15N], 0.8 mM; EDTA 10 uM; potassium phosphate 1.06 mM; protease inhibitor complete cocktail 0.16 % w/w; sodium azide 0.02%; sodium chloride 155.2 mM; sodium phosphate 2.97 mM; H2O 95%; D2O, [U-2H], 5%

sample_2: foldU5, [U-100% 13C; U-100% 15N], 0.4 mM; Pf1 phage 10 mg/mL; EDTA 10 mM; potassium phosphate 1.06 mM; protease inhibitor complete cocktail 0.16 % w/w; sodium azide 0.02%; 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:

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 HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D (H)N(CA)NHsample_1isotropicsample_conditions_1
3D H(NCA)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSY aliphaticsample_1isotropicsample_conditions_1
3D HCCH-TOCSY aromaticsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HNHAHBsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY 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
3D J-HNCOsample_1isotropicsample_conditions_1
3D J-HNCOsample_2anisotropicsample_conditions_1
3D J-HN(CO)CAsample_1isotropicsample_conditions_1
3D J-HN(CO)CAsample_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 v2.01.32, Kobayashi, N. - chemical shift assignment, 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 v3.5, 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 shifts
SPARKY: Backbone or all simulated shifts