BMRB Entry 36332

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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/BMR36332
MolProbity Validation Chart

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Title:
Solution NMR structure of NF4; de novo designed protein with a novel fold
Deposition date:
2020-03-24
Original release date:
2021-03-29
Authors:
Kobayashi, N.; Nagashima, T.; Minami, S.; Koga, R.; Chikenji, T.; 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, 125 residues, 14838.945 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: GSEEIRELVRKIYETVRKEN PNVKILIFIIFTSDGTIKVI IVIIADDPNDAKRIVKKIQE RFPKLTIKQSRNEEEAEKRI QKELEERNPNAEIQVVRSED ELKEILDKLDEKKGSWSLEH HHHHH

Data sets:
Data typeCount
13C chemical shifts540
15N chemical shifts123
1H chemical shifts835

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 125 residues - 14838.945 Da.

1   GLYSERGLUGLUILEARGGLULEUVALARG
2   LYSILETYRGLUTHRVALARGLYSGLUASN
3   PROASNVALLYSILELEUILEPHEILEILE
4   PHETHRSERASPGLYTHRILELYSVALILE
5   ILEVALILEILEALAASPASPPROASNASP
6   ALALYSARGILEVALLYSLYSILEGLNGLU
7   ARGPHEPROLYSLEUTHRILELYSGLNSER
8   ARGASNGLUGLUGLUALAGLULYSARGILE
9   GLNLYSGLULEUGLUGLUARGASNPROASN
10   ALAGLUILEGLNVALVALARGSERGLUASP
11   GLULEULYSGLUILELEUASPLYSLEUASP
12   GLULYSLYSGLYSERTRPSERLEUGLUHIS
13   HISHISHISHISHIS

Samples:

sample_1: NF4, [U-100% 13C; U-100% 15N], 0.45 mM; potassium phosphate 1.1 mM; sodium chloride 137 mM; sodium phosphate 5.6 mM; H2O 95%; D2O, [U-2H], 5%

sample_2: NF4, [U-100% 13C; U-100% 15N], 0.2 mM; Pf1 phage 10 mg/mL; potassium phosphate 1.1 mM; sodium chloride 137 mM; sodium phosphate 5.6 mM; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 145.5 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 HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSY aliphaticsample_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, Kobayashi, N. - peak picking

NMRPipe v2017, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - data analysis

TALOS v2017, Cornilescu, Delaglio and Bax - data analysis

TopSpin v3.2, 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

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