BMRB Entry 36264

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR36264
MolProbity Validation Chart

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Title:
Solution structure of the intermembrane space domain of the mitochondrial import protein Tim21 from S. cerevisiae
Deposition date:
2019-06-13
Original release date:
2020-07-15
Authors:
Bala, S.; Shinya, S.; Srivastava, A.; Shimada, A.; Kobayashi, N.; Kojima, C.; Tama, F.; Miyashita, O.; Kohda, D.
Citation:

Citation: Bala, S.; Shinya, S.; Srivastava, A.; Ishikawa, M.; Shimada, A.; Kobayashi, N.; Kojima, C.; Tama, F.; Miyashita, O.; Kohda, D.. "Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study."  Biochim. Biophys. Acta Gen. Subj. 1864, 129418-129418 (2019).
PubMed: 31449839

Assembly members:

Assembly members:
entity_1, polymer, 115 residues, 13571.599 Da.

Natural source:

Natural source:   Common Name: Baker's yeast   Taxonomy ID: 559292   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces Saccharomyces cerevisiae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21   Vector: pET28b(+)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSDTQLFNRAVSMVEKNKDI RSLLQCDDGITGKERLKAYG ELITNDKWTRNRPIVSTKKL DKEGRTHHYMRFHVESKKKI ALVHLEAKESKQNYQPDFIN MYVDVPGEKRYYLIK

Data sets:
Data typeCount
13C chemical shifts494
15N chemical shifts120
1H chemical shifts786

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 115 residues - 13571.599 Da.

1   GLYSERASPTHRGLNLEUPHEASNARGALA
2   VALSERMETVALGLULYSASNLYSASPILE
3   ARGSERLEULEUGLNCYSASPASPGLYILE
4   THRGLYLYSGLUARGLEULYSALATYRGLY
5   GLULEUILETHRASNASPLYSTRPTHRARG
6   ASNARGPROILEVALSERTHRLYSLYSLEU
7   ASPLYSGLUGLYARGTHRHISHISTYRMET
8   ARGPHEHISVALGLUSERLYSLYSLYSILE
9   ALALEUVALHISLEUGLUALALYSGLUSER
10   LYSGLNASNTYRGLNPROASPPHEILEASN
11   METTYRVALASPVALPROGLYGLULYSARG
12   TYRTYRLEUILELYS

Samples:

sample_1: Tim21, [U-13C; U-15N], 323 uM; TRIS 20 mM; sodium chloride 50 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 50 mM; pH: 6.5; pressure: 1 atm; temperature: 300 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - chemical shift assignment, structure calculation

MagRO-NMRView, Naohiro Kobayashi, Osaka University - chemical shift assignment, data analysis, peak picking

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

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

  • Bruker AVANCE III 600 MHz
  • Bruker AVANCE III 950 MHz

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