BMRB Entry 18778

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18778
MolProbity Validation Chart

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Title:
Solution structure of LIMD2
Deposition date:
2012-10-10
Original release date:
2014-04-14
Authors:
Talebzadeh Farooji, Mehdi; Peng, Hongzhuang; Rauscher, Frank; Borden, Katherine; Osborne, Michael
Citation:

Citation: Talebzadeh Farooji, Mehdi. "Solution Structure of LIMD2"  .

Assembly members:

Assembly members:
LIMD2, polymer, 72 residues, 8318.710 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: Humans   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET47b+

Entity Sequences (FASTA):

Entity Sequences (FASTA):
LIMD2: RAQVKETCAACQKTVYPMER LVADKLIFHNSCFCCKHCHT KLSLGSYAALHGEFYCKPHF QQLFKSKGNYDE

Data sets:
Data typeCount
13C chemical shifts161
15N chemical shifts64
1H chemical shifts369

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1LIMD21
2ZINC ION_12
3ZINC ION_22

Entities:

Entity 1, LIMD2 72 residues - 8318.710 Da.

1   ARGALAGLNVALLYSGLUTHRCYSALAALA
2   CYSGLNLYSTHRVALTYRPROMETGLUARG
3   LEUVALALAASPLYSLEUILEPHEHISASN
4   SERCYSPHECYSCYSLYSHISCYSHISTHR
5   LYSLEUSERLEUGLYSERTYRALAALALEU
6   HISGLYGLUPHETYRCYSLYSPROHISPHE
7   GLNGLNLEUPHELYSSERLYSGLYASNTYR
8   ASPGLU

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1   ZN

Samples:

LIMD2-1: LIMD2, [U-99% 13C; U-99% 15N], 300 – 500 uM; sodium phosphate 50 mM; sodium chloride 100 mM; TCEP 1 mM; H2O 90%; D2O 10%

LIMD2-2: LIMD2, [U-99% 15N], 300 – 500 uM; sodium phosphate 50 mM; sodium chloride 100 mM; TCEP 1 mM; H2O 90%; D2O 10%

LIMD2-3: LIMD2300 – 500 uM; sodium phosphate 50 mM; sodium chloride 100 mM; TCEP 1 mM; D2O 100%

LIMD2-4: LIMD2, [U-99% 13C; U-99% 15N], 300 – 500 uM; sodium phosphate 50 mM; sodium chloride 100 mM; TCEP 1 mM; D2O 100%

sample_conditions_1: ionic strength: 0.1 M; pH: 7.2; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D HNCACBLIMD2-1isotropicsample_conditions_1
2D 1H-15N HSQCLIMD2-2isotropicsample_conditions_1
2D 1H-13C HSQCLIMD2-1isotropicsample_conditions_1
2D DQF-COSYLIMD2-3isotropicsample_conditions_1
2D 1H-1H TOCSYLIMD2-3isotropicsample_conditions_1
2D 1H-1H NOESYLIMD2-3isotropicsample_conditions_1
3D HCCH-TOCSYLIMD2-4isotropicsample_conditions_1
3D 1H-15N NOESYLIMD2-2isotropicsample_conditions_1
3D 1H-13C NOESYLIMD2-4isotropicsample_conditions_1
3D H(CCO)NHLIMD2-1isotropicsample_conditions_1
3D CBCA(CO)NHLIMD2-1isotropicsample_conditions_1
3D HBHA(CO)NHLIMD2-1isotropicsample_conditions_1
3D HNHBLIMD2-2isotropicsample_conditions_1

Software:

VNMRJ, Varian - collection

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

SPARKY, Goddard - chemical shift assignment

ARIA v2.3, Linge, O'Donoghue and Nilges - Automated chemical shift asignment, structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

Molmol, Koradi, Billeter and Wuthrich - Visualization

PyMol, Warren Delano - Visualization

NMR spectrometers:

  • Varian INOVA 600 MHz

Related Database Links:

PDB
DBJ BAC03855 BAC25371 BAC27866 BAC33928 BAE39448
GB AAH04400 AAH51812 AAH68130 AAH98855 AAI16117
REF NP_001020886 NP_001035602 NP_001231640 NP_001247518 NP_085053
SP Q1LZA7 Q4KM31 Q8BGB5 Q9BT23
TPG DAA18353
AlphaFold Q1LZA7 Q4KM31 Q8BGB5 Q9BT23

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