BMRB Entry 30696

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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/BMR30696
MolProbity Validation Chart

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Title:
Solution NMR structure of Dictyostelium discoideum Skp1A (truncated) dimer
Deposition date:
2019-12-10
Original release date:
2020-04-13
Authors:
Kim, H.; Eletsky, A.; West, C.
Citation:

Citation: Kim, H.; Eletsky, A.; Gonzalez, K.; van der Wel, H.; Strauch, E.; Prestegard, J.; West, C.. "Skp1 Dimerization Conceals Its F-Box Protein Binding Site"  Biochemistry 59, 1527-1536 (2020).
PubMed: 32227851

Assembly members:

Assembly members:
entity_1, polymer, 116 residues, 12998.891 Da.

Natural source:

Natural source:   Common Name: Slime mold   Taxonomy ID: 44689   Superkingdom: Eukaryota   Kingdom: not available   Genus/species: Dictyostelium discoideum

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SLVKLESSDEKVFEIEKEIA CMSVTIKNMIEDIGESDSPI PLPNVTSTILEKVLDYCRHH HQHPGGSGLDDIPPYDRDFC KVDQPTLFELILAANYLDIK PLLDVTCKTVANMIRG

Data typeCount
13C chemical shifts531
15N chemical shifts124
1H chemical shifts851

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_1, 11
2entity_1, 21

Entities:

Entity 1, entity_1, 1 116 residues - 12998.891 Da.

1   SERLEUVALLYSLEUGLUSERSERASPGLU
2   LYSVALPHEGLUILEGLULYSGLUILEALA
3   CYSMETSERVALTHRILELYSASNMETILE
4   GLUASPILEGLYGLUSERASPSERPROILE
5   PROLEUPROASNVALTHRSERTHRILELEU
6   GLULYSVALLEUASPTYRCYSARGHISHIS
7   HISGLNHISPROGLYGLYSERGLYLEUASP
8   ASPILEPROPROTYRASPARGASPPHECYS
9   LYSVALASPGLNPROTHRLEUPHEGLULEU
10   ILELEUALAALAASNTYRLEUASPILELYS
11   PROLEULEUASPVALTHRCYSLYSTHRVAL
12   ALAASNMETILEARGGLY

Samples:

sample_1: DDSkp1, [U-90% 13C; U-90% 15N], 0.5 mM; MES 50 mM; NaCl 50 mM; DTT 5 mM; sodium azide 0.05%

sample_conditions_1: ionic strength: 50 mM; pH: 6.0; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D [15N, 1H]-HSQCsample_1isotropicsample_conditions_1
2D [13C, 1H] CT-HSQC aliphaticsample_1isotropicsample_conditions_1
2D [13C, 1H] CT-HSQC aromaticsample_1isotropicsample_conditions_1
3D 13C/15N-edited [1H,1H] NOESYsample_1isotropicsample_conditions_1
3D TROSY-HNCACBsample_1isotropicsample_conditions_1
3D (H)CCH-COSY aromaticsample_1isotropicsample_conditions_1
3D (H)CCH-COSY aliphaticsample_1isotropicsample_conditions_1
3D (H)CCH-TOCSY aliphaticsample_1isotropicsample_conditions_1
3D 13C/15N-filtered 13C/15N-edited [1H,1H] NOESYsample_1isotropicsample_conditions_1
2D long-range [15N, 1H]-HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D (HCA)CONHsample_1isotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - collection, processing

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

CARA, Keller and Wuthrich - chemical shift assignment, data analysis, peak picking

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

VNMR, Varian - collection

TALOS, Cornilescu, Delaglio and Bax - data analysis

PSVS, Bhattacharya and Montelione - data analysis

NMR spectrometers:

  • Bruker AVANCE NEO 800 MHz
  • Agilent VNMRS 600 MHz

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