BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 18642

Title: Protein structure   PubMed: 23770917

Deposition date: 2012-08-06 Original release date: 2013-06-10

Authors: Mercier, Pascal; Spratt, Donald; Manczyk, Noah; Shaw, Gary

Citation: Spratt, Donald; Julio Martinez-Torres, R.; Noh, Yeong; Mercier, Pascal; Manczyk, Noah; Barber, Kathryn; Aguirre, Jacob; Burchell, Lynn; Purkiss, Andrew; Walden, Helen; Shaw, Gary. "A molecular explanation for the recessive nature of parkin-linked Parkinson's disease."  Nat. Commun. 4, 1983-1983 (2013).

Assembly members:
Protein, polymer, 68 residues, 7669.769 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:   Common Name: Fruit fly   Taxonomy ID: 7227   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Drosophila melanogaster

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
Protein: GSAEARWDEASNVTIKVSTK PCPKCRTPTERDGGCMHMVC TRAGCGFEWCWVCQTEWTRD CMGAHWFG

Data sets:
Data typeCount
13C chemical shifts256
15N chemical shifts63
1H chemical shifts388

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Protein1
2ZINC ION_12
3ZINC ION_22

Entities:

Entity 1, Protein 68 residues - 7669.769 Da.

N-terminal GS sequence results from the cleavage site

1   GLYSERALAGLUALAARGTRPASPGLUALA
2   SERASNVALTHRILELYSVALSERTHRLYS
3   PROCYSPROLYSCYSARGTHRPROTHRGLU
4   ARGASPGLYGLYCYSMETHISMETVALCYS
5   THRARGALAGLYCYSGLYPHEGLUTRPCYS
6   TRPVALCYSGLNTHRGLUTRPTHRARGASP
7   CYSMETGLYALAHISTRPPHEGLY

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: TRIS 20 mM; sodium chloride 120 mM; DTT 5 mM; Protein, [U-98% 15N], 500 uM; H2O 90%; D2O 10%

sample_2: TRIS 20 mM; sodium chloride 120 mM; DTT 5 mM; Protein, [U-98% 13C; U-98% 15N], 500 uM; H2O 90%; D2O 10%

sample_3: TRIS 20 mM; sodium chloride 120 mM; DTT 5 mM; Protein, [U-98% 13C; U-98% 15N], 500 uM; D2O 100%

sample_conditions_1: ionic strength: 0.120 M; pH: 7.25; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_3isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNHAsample_2isotropicsample_conditions_1
3D C(CO)NHsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
2D (HB)CB(CGCD)HDsample_2isotropicsample_conditions_1
2D (HB)CB(CGCDCE)HEsample_2isotropicsample_conditions_1

Software:

VNMRJ vVarian VnmrJ 2.2D, Varian - collection

NMRPipe v2011.084.20.33, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRDraw vVer 5.7 Rev 2011.084.20.33, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v8.2.33 with Java 1.6.0_31, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

X-PLOR NIH v2.31, Schwieters, Kuszewski, Tjandra and Clore - refinement

TALOS vTALOSPlus, Cornilescu, Delaglio and Bax - geometry optimization

Procheck v3.5.4, Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Tho - data analysis

NMR spectrometers:

  • Varian INOVA 600 MHz

Related Database Links:

BMRB 18990
PDB
GB AAL13983 AAM18800 AAM43930 AAN12154 AAN12155
REF NP_730600 NP_730601 XP_001956965 XP_001973584 XP_001984548

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts