BMRB Entry 25088

Click here to enlarge.

PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25088
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Title:
NMR solution structure of the Ubiquitin like domain (UBL) of DNA-damage-inducible 1 protein (Ddi1)
Deposition date:
2014-07-14
Original release date:
2015-03-23
Authors:
Nowicka, Urszula; Fushman, David; Chen, Tony
Citation:

Citation: Nowicka, Urszula; Zhang, Daoning; Walker, Olivier; Castaneda, Calos; Krutauz, Daria; Chen, Tony; Reis, Noa; Glickman, Michael; Fushman, David. "DNA-Damage-Inducible 1 Protein (Ddi1) Contains an Uncharacteristic Ubiquitin-like Domain that Binds Ubiquitin"  Structure 23, 542-557 (2015).
PubMed: 25703377

Assembly members:

Assembly members:
Ddi1UBL, polymer, 79 residues, 8827.999 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: pQE30

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Ddi1UBL: DLTISNELTGEIYGPIEVSE DMALTDLIALLQADCGFDKT KHDLYYNMDILDSNRTQSLK ELGLKTDDLLLIRGKISNS

Data sets:
Data typeCount
1H chemical shifts571
13C chemical shifts331
15N chemical shifts84

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Ddi1UBL1

Entities:

Entity 1, Ddi1UBL 79 residues - 8827.999 Da.

1   ASPLEUTHRILESERASNGLULEUTHRGLY
2   GLUILETYRGLYPROILEGLUVALSERGLU
3   ASPMETALALEUTHRASPLEUILEALALEU
4   LEUGLNALAASPCYSGLYPHEASPLYSTHR
5   LYSHISASPLEUTYRTYRASNMETASPILE
6   LEUASPSERASNARGTHRGLNSERLEULYS
7   GLULEUGLYLEULYSTHRASPASPLEULEU
8   LEUILEARGGLYLYSILESERASNSER

Samples:

sample_1: Ddi1UBL, [U-100% 15N], 1 mM; D2O, [U-99% 2H], 5%; H2O 95%; sodium phosphate 20 mM; TCEP 3 mM

sample_2: Ddi1UBL, [U-100% 13C; U-100% 15N], 1 mM; D2O, [U-99% 2H], 5%; H2O 95%; sodium phosphate 20 mM; TCEP 3 mM

sample_3: Ddi1UBL, [U-100% 15N], 1 mM; D2O, [U-99% 2H], 5%; H2O 45%; sodium phosphate 10 mM; TCEP 3 mM; C12E5 5%; n-hexanol 45%

sample_conditions_1: temperature: 295.5 K; pH: 6.8; pressure: 1 atm; ionic strength: 10 mM

sample_conditions_2: temperature: 315 K; pH: 6.8; pressure: 1 atm; ionic strength: 10 mM

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HN(CA)COsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D C(CO)NHsample_2isotropicsample_conditions_1
RDCsample_3isotropicsample_conditions_1
RDCsample_3isotropicsample_conditions_2

Software:

CARA v1.8.1, Keller and Wuthrich - peak picking, chemical shift assignment

TOPSPIN v2.1, Bruker Biospin - collection, processing, data analysis

ARIA v2.1, Linge, O'Donoghue and Nilges - structure solution, refinement

TALOS vTALOS+, Cornilescu, Delaglio and Bax - backbone torsion angles prediction

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

UNP P40087
PDB
DBJ GAA22973
EMBL CAY79329
GB AAB64670 AAB82066 AAC18522 AAT92964 AHY75700
REF NP_011070
SP P40087
TPG DAA07804
AlphaFold D3DM50 P40087

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