BMRB Entry 36334

Title:
Solution NMR structure of NF3; de novo designed protein with a novel fold
Deposition date:
2020-03-24
Original release date:
2021-03-29
Authors:
Kobayashi, N.; Sugiki, T.; Fujiwara, T.; Minami, S.; Koga, R.; Chikenji, G.; Koga, N.
Citation:

Citation: Minami, S.; Kobayashi, N.; Sugiki, T.; Nagashima, T.; Fujiwara, T.; Koga, R.; Chikenji, G.; Koga, N.. "Exploration of novel alpha-beta protein folds through de novo design"  Nat. Struct. Mol. Biol. 30, 1132-1140 (2023).
PubMed: 37400653

Assembly members:

Assembly members:
entity_1, polymer, 110 residues, 12997.888 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

Data sets:
Data typeCount
13C chemical shifts468
15N chemical shifts107
1H chemical shifts775

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 110 residues - 12997.888 Da.

1   GLYSERASPGLUGLUILEARGLYSLYSLEU
2   GLUGLULEUALALYSARGLYSGLYLYSASP
3   LEUGLNLEUARGARGTYRASNASPPROASN
4   GLUVALGLULYSSERILEARGGLUALALEU
5   LYSLYSGLYARGTHRLEUILEILEILEILE
6   ASNGLYVALPHEVALVALVALSERTHRASP
7   GLUASPLEUILEARGGLUILELYSARGLEU
8   ILELYSGLUSERASNPROASNLYSLYSTHR
9   LEUASPVALTHRTHRGLUGLUASPLEUGLU
10   GLUVALLEUARGARGILELYSLYSGLYSER
11   TRPSERLEUGLUHISHISHISHISHISHIS

Samples:

sample_1: NF3, [U-100% 13C; U-100% 15N], 0.9 mM; potassium phosphate 7.4 mM; sodium chloride 50 mM; sodium phosphate 1.1 mM; H2O 95%; D2O, [U-2H], 5%

sample_2: NF3, [U-100% 13C; U-100% 15N], 0.2 mM; Pf1 phage 6 mg/mL; potassium phosphate 7.4 mM; sodium chloride 50 mM; sodium phosphate 1.1 mM; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 58.5 mM; pH: 6.0; 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 BEST-HN(CO)CACBsample_1isotropicsample_conditions_1
3D HCCH-TOCSY aliphaticsample_1isotropicsample_conditions_1
3D HCCH-TOCSY aromaticsample_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

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 v2.01.38, 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 800 MHz

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