BMRB Entry 30890

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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/BMR30890
MolProbity Validation Chart

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Title:
Solution NMR structure of de novo designed protein 0515
Deposition date:
2021-03-24
Original release date:
2021-12-06
Authors:
Ramelot, T.; Hao, J.; Baker, D.; Montelione, G.
Citation:

Citation: Anishchenko, Ivan; Pellock, Samuel; Chidyausiku, Tamuka; Ramelot, Theresa; Ovchinnikov, Sergey; Hao, Jingzhou; Bafna, Khushboo; Norn, Christoffer; Kang, Alex; Bera, Asim; DiMaio, Frank; Carter, Lauren; Chow, Cameron; Montelione, Gaetano; Baker, David. "De novo protein design by deep network hallucination"  Nature 600, 547-552 (2021).
PubMed: 34853475

Assembly members:

Assembly members:
entity_1, polymer, 100 residues, 11474.791 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 BL21(DE3)   Vector: pET28b(+)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MDFTERLDRLVKYAKEIAKW YKESGDPDFANSVDNVLGHL ENIRKAFKHGDPARAMDHVS NVVGSLDSIQTSFKQTGNPE IATRWQELTQEVRELYAYLG

Data sets:
Data typeCount
13C chemical shifts419
15N chemical shifts102
1H chemical shifts677

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 100 residues - 11474.791 Da.

1   METASPPHETHRGLUARGLEUASPARGLEU
2   VALLYSTYRALALYSGLUILEALALYSTRP
3   TYRLYSGLUSERGLYASPPROASPPHEALA
4   ASNSERVALASPASNVALLEUGLYHISLEU
5   GLUASNILEARGLYSALAPHELYSHISGLY
6   ASPPROALAARGALAMETASPHISVALSER
7   ASNVALVALGLYSERLEUASPSERILEGLN
8   THRSERPHELYSGLNTHRGLYASNPROGLU
9   ILEALATHRARGTRPGLNGLULEUTHRGLN
10   GLUVALARGGLULEUTYRALATYRLEUGLY

Samples:

sample_1: protein, [U-13C; U-15N], 0.9 ± .1 mM; HEPES 25 ± 2 mM; sodium chloride 50 ± 5 mM; sodium azide 0.02 ± .005 %

sample_2: protein, [U-5% 13C; U-15N], 0.3 ± .05 mM; HEPES 25 ± 2 mM; sodium chloride 50 ± 5 mM; sodium azide 0.02 ± .005 %

sample_conditions_1: ionic strength: 50 mM; pH: 7.2; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCACB-Bsample_1isotropicsample_conditions_1
3D HN(CO)CACB-Bsample_1isotropicsample_conditions_1
3D HNCO-Bsample_1isotropicsample_conditions_1
3D HNCA-Bsample_1isotropicsample_conditions_1
3D HBHAsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D TOCSY-NHSQCsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D CCH-TOCSY aliphsample_1isotropicsample_conditions_1
3D CCH-TOCSY aromsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC ctsample_2isotropicsample_conditions_1

Software:

CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CYANA v3.98.13, Guntert, Mumenthaler and Wuthrich - structure calculation

I-PINE, Lee, Bahrami, Dashti, Eghbalnia, Tonelli, Westler and Markley - chemical shift assignment

NMRFAM-SPARKY v1.37, Lee W, Tonelli M, Markley JL - peak picking

NMRPipe vv10.9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

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