BMRB Entry 36652

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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/BMR36652
MolProbity Validation Chart

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

Title:
Ubiquitin(native) from Oryza sativa subsp. japonica (Rice)
Deposition date:
2024-03-24
Original release date:
2026-02-06
Authors:
Sri Teja, A.; Sarma, S.
Citation:

Citation: Adhada, Sri; Sarma, Siddhartha. "Slow Conformational Exchange between Partially Folded and Near-Native States of Ubiquitin: Evidence for a Multistate Folding Model."  Biochemistry 63, 2565-2579 (2024).
PubMed: 39351677

Assembly members:

Assembly members:
Ubiquitin, polymer, 77 residues, 8667.964 Da.

Natural source:

Natural source:   Common Name: Asian cultivated rice   Taxonomy ID: 39947   Superkingdom: Eukaryota   Kingdom: Viridiplantae   Genus/species: Oryza sativa

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Ubiquitin: MMQIFVKTLTGKTITLEVES SDTIDNVKAKIQDKEGIPPD QQRLIFAGKQLEDGRTLADY NIQKESTLHLVLRLRGG

Data sets:
Data typeCount
13C chemical shifts327
15N chemical shifts82
1H chemical shifts538

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 77 residues - 8667.964 Da.

1   METMETGLNILEPHEVALLYSTHRLEUTHR
2   GLYLYSTHRILETHRLEUGLUVALGLUSER
3   SERASPTHRILEASPASNVALLYSALALYS
4   ILEGLNASPLYSGLUGLYILEPROPROASP
5   GLNGLNARGLEUILEPHEALAGLYLYSGLN
6   LEUGLUASPGLYARGTHRLEUALAASPTYR
7   ASNILEGLNLYSGLUSERTHRLEUHISLEU
8   VALLEUARGLEUARGGLYGLY

Samples:

sample_1: Ubiquitin from Rice (Oryza sativa), [U-15N], 1 ± 0.1 mM; NaCl 25 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: Ubiquitin from Rice (Oryza sativa), [U-13C; U-15N], 1 ± 0.1 mM; NaCl 25 mM; H2O 90%; D2O, [U-2H], 10%

sample_3: Ubiquitin from Rice (Oryza sativa) 1 ± 0.1 mM; NaCl 25 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 25 mM; pH: 6.8; pressure: 1 bar; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D C(CO)NHsample_2isotropicsample_conditions_1
3D 1H-15N TOCSYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D H(CCO)NHsample_2isotropicsample_conditions_1
1D DOSYsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1

Software:

CcpNmr Analysis v2.5.2, CCPN - chemical shift assignment

CYANA v3.98.15, Guntert, Mumenthaler and Wuthrich - structure calculation

X-PLOR NIH v3.4, Schwieters, Kuszewski, Tjandra and Clore - refinement

VnmrJ v4.2, Varian - collection

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

NMR spectrometers:

  • Agilent Direct Drive 600 MHz
  • Bruker AVANCE 700 MHz

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