BMRB Entry 36333

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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/BMR36333
MolProbity Validation Chart

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Title:
Solution NMR structure of NF8 (knot fold); 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, 88 residues, 10296.638 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: GTILIFLDKNKEQAEKLAKE VGVTEIYESDNLEELYREIK ERIERENPNATILTVTDPNE LKKIQDEGKVDRIILLIKGS LEHHHHHH

Data sets:
Data typeCount
13C chemical shifts371
15N chemical shifts84
1H chemical shifts588

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 88 residues - 10296.638 Da.

1   GLYTHRILELEUILEPHELEUASPLYSASN
2   LYSGLUGLNALAGLULYSLEUALALYSGLU
3   VALGLYVALTHRGLUILETYRGLUSERASP
4   ASNLEUGLUGLULEUTYRARGGLUILELYS
5   GLUARGILEGLUARGGLUASNPROASNALA
6   THRILELEUTHRVALTHRASPPROASNGLU
7   LEULYSLYSILEGLNASPGLUGLYLYSVAL
8   ASPARGILEILELEULEUILELYSGLYSER
9   LEUGLUHISHISHISHISHISHIS

Samples:

sample_1: NF8, [U-100% 13C; U-100% 15N], 0.95 mM; potassium phosphate 5.7 mM; sodium chloride 50 mM; sodium phosphate 4.3 mM; H2O 95%; D2O, [U-2H], 5%

sample_2: NF8, [U-100% 13C; U-100% 15N], 0.2 mM; Pf1 phage 10 mg/mL; potassium phosphate 5.7 mM; sodium chloride 50 mM; sodium phosphate 4.3 mM; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 56.5 mM; pH: 6.8; 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