BMRB Entry 17238

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17238
MolProbity Validation Chart

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Title:
NMR structure of the UBA domain of S. cerevisiae Dcn1
Deposition date:
2010-10-05
Original release date:
2012-07-25
Authors:
Burschowsky, Daniel; Rudolf, Fabian; Mattle, Daniel; Peter, Matthias; Wider, Gerhard
Citation:

Citation: Burschowsky, Daniel; Rudolf, Fabian; Mattle, Daniel; Peter, Matthias; Wider, Gerhard. "Structural analysis of the ubiquitin-associated domain (UBA) of yeast Dcn1 in complex with ubiquitin (WORKING TITLE)"  .

Assembly members:

Assembly members:
Dcn1-UBA, polymer, 59 residues, 6914.6 Da.

Natural source:

Natural source:   Common Name: baker's yeast   Taxonomy ID: 4932   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pGEX-4T

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Dcn1-UBA: GSIKRKDASPEQEAIESFTS LTKCDPKVSRKYLQRNHWNI NYALNDYYDKEIGTFTDEV

Data sets:
Data typeCount
13C chemical shifts200
15N chemical shifts65
1H chemical shifts417

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1Dcn1-UBA1

Entities:

Entity 1, Dcn1-UBA 59 residues - 6914.6 Da.

N-terminal residues number 4 and 5 (GS) are non-native and leftovers from thrombin cleavage

1   GLYSERILELYSARGLYSASPALASERPRO
2   GLUGLNGLUALAILEGLUSERPHETHRSER
3   LEUTHRLYSCYSASPPROLYSVALSERARG
4   LYSTYRLEUGLNARGASNHISTRPASNILE
5   ASNTYRALALEUASNASPTYRTYRASPLYS
6   GLUILEGLYTHRPHETHRASPGLUVAL

Samples:

UBA-13C15N: Dcn1-UBA, [U-80% 13C; U-90% 15N], 0.6 mM; potassium phosphate 15 mM; potassium phosphate 110 mM; DTT 2 mM; CHAPS 2 mM; sodium azide 0.05%; H2O 95%; D2O 5%

UBA-15N: Dcn1-UBA, [U-90% 15N], 0.55 mM; potassium phosphate 15 mM; potassium phosphate 110 mM; DTT 2 mM; CHAPS 2 mM; sodium azide 0.05%; H2O 95%; D2O 5%

NMR_Standard_Conditions: ionic strength: 157 mM; pH: 6.15; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
3D HNCAUBA-13C15NisotropicNMR_Standard_Conditions
3D CBCA(CO)NHUBA-13C15NisotropicNMR_Standard_Conditions
3D HCCH-TOCSYUBA-13C15NisotropicNMR_Standard_Conditions
3D 1H-15N NOESYUBA-15NisotropicNMR_Standard_Conditions
3D 1H-13C NOESYUBA-13C15NisotropicNMR_Standard_Conditions
3D 1H-13Caro NOESYUBA-13C15NisotropicNMR_Standard_Conditions
2D 1H-15N HSQCUBA-15NisotropicNMR_Standard_Conditions

Software:

UNIO v1.0.4, Herrmann - chemical shift assignment, peak picking

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

CYANA v2, Guntert, Mumenthaler and Wuthrich - structure solution

xwinnmr, Bruker Biospin - collection, processing

TOPSPIN v2.0, Bruker Biospin - processing

CARA v1.8.4, Keller - data analysis

NMR spectrometers:

  • Bruker DRX 500 MHz
  • Bruker DRX 600 MHz
  • Bruker DRX 750 MHz
  • Bruker Avance 900 MHz

Related Database Links:

BMRB 17239
PDB
DBJ GAA25010
EMBL CAA61706 CAA62639 CAA97697 CAY81363
GB AAB82374 AHY78522 AJP40299 AJV46201 AJV46655
REF NP_013229
SP Q12395
TPG DAA09439
AlphaFold Q12395

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