BMRB Entry 25657

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25657
MolProbity Validation Chart

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Title:
Proteasome protein fragment
Deposition date:
2015-06-10
Original release date:
2016-02-22
Authors:
Chen, Xiang; Vannoy, Jacob; Walters, Kylie
Citation:

Citation: Chen, Xiang; Shi, Yanhong; Shi, Yuan; Elsasser, Suzanne; Vannoy, Jacob; Finley, Daniel; Tarasov, Sergey; Walters, Kylie. "Structures of Rpn1:ubiquitin and Rpn1:K48 diubiquitin define Rpn1 as a novel proteasome ubiquitin receptor."  .

Assembly members:

Assembly members:
protein, polymer, 131 residues, 13636.695 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: Pgex4t1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
protein: DTKISSAAILGLGIAFAGSK NDEVLGLLLPIAASTDLPIE TAAMASLALAHVFVGTCNGD ITTSIMDNFLERTAIELKTD WVRFLALALGILYMGQGEQV DDVLETISAIEHPMTSAIEV LVGSCAYTGTG

Data sets:
Data typeCount
13C chemical shifts303
15N chemical shifts63
1H chemical shifts657

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity1

Entities:

Entity 1, entity 131 residues - 13636.695 Da.

1   ASPTHRLYSILESERSERALAALAILELEU
2   GLYLEUGLYILEALAPHEALAGLYSERLYS
3   ASNASPGLUVALLEUGLYLEULEULEUPRO
4   ILEALAALASERTHRASPLEUPROILEGLU
5   THRALAALAMETALASERLEUALALEUALA
6   HISVALPHEVALGLYTHRCYSASNGLYASP
7   ILETHRTHRSERILEMETASPASNPHELEU
8   GLUARGTHRALAILEGLULEULYSTHRASP
9   TRPVALARGPHELEUALALEUALALEUGLY
10   ILELEUTYRMETGLYGLNGLYGLUGLNVAL
11   ASPASPVALLEUGLUTHRILESERALAILE
12   GLUHISPROMETTHRSERALAILEGLUVAL
13   LEUVALGLYSERCYSALATYRTHRGLYTHR
14   GLY

Samples:

sample_1: protein, [U-100% 13C; U-100% 15N; U-80% 2H], 0.7 mM; HEPES 50 mM; sodium chloride 50 mM; DTT 2 mM; EDTA 1 mM; sodium azide 0.1%; H2O 95%; D2O 5%

sample_2: protein, [U-100% 15N], 0.7 mM; HEPES 50 mM; sodium chloride 50 mM; DTT 2 mM; EDTA 1 mM; sodium azide 0.1%; H2O 95%; D2O 5%

sample_3: protein, [U-100% 13C], 0.7 mM; HEPES 50 mM; sodium chloride 50 mM; DTT 2 mM; EDTA 1 mM; sodium azide 0.1%; D2O 100%

sample_conditions_1: ionic strength: 50 mM; pH: 6.7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_3isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

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

XEASY, Bartels et al. - chemical shift assignment, data analysis, peak picking

TALOS, Cornilescu, Delaglio and Bax - data analysis

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

ProcheckNMR, Laskowski and MacArthur - refinement

NMR spectrometers:

  • Bruker Avance 850 MHz
  • Bruker Avance 900 MHz
  • Bruker Avance 700 MHz
  • Varian INOVA 800 MHz

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