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Biological Magnetic Resonance Data Bank


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BMRB Entry 15477

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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/BMR15477
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Title: Solution structure of the extracellular domain of Prod1, a protein implicated in proximodistal identity during amphibian limb regeneration   PubMed: 19771161

Deposition date: 2007-09-19 Original release date: 2009-10-14

Authors: Garza-Garcia, Acely; Harris, Richard; Esposito, Diego; Driscoll, Paul

Citation: Garza-Garcia, Acely; Harris, Richard; Esposito, Diego; Gates, Phillip; Driscoll, Paul. "Solution structure and phylogenetics of Prod1, a member of the three-finger protein superfamily implicated in salamander limb regeneration."  PLoS One 4, 7123-. (2009).

Assembly members:
Prod1, polymer, 91 residues, 10208.4 Da.

Natural source:   Common Name: Eastern newt   Taxonomy ID: 8316   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Notophthalmus viridescens

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

Entity Sequences (FASTA):
Prod1: MGSSHHHHHHSSGLVPRGSH MALKCFTRNGDDRTVTTCAE EQTRCLFVQLPYSEIQECKT VQQCAEVLEEVTAIGYPAKC CCEDLCNRSEQ

Data sets:
Data typeCount
13C chemical shifts300
15N chemical shifts69
1H chemical shifts461

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1Prod11

Entities:

Entity 1, Prod1 91 residues - 10208.4 Da.

His Tag MGSSHHHHHH SSGLVPRGSH M Protein Sequence ALKCFTRNGDDRTVTTCAEEQTRCLFVQLPYSEIQECKTVQQCAEVLEEVTAIGYPAKCCCEDLCNRSEQ

1   METGLYSERSERHISHISHISHISHISHIS
2   SERSERGLYLEUVALPROARGGLYSERHIS
3   METALALEULYSCYSPHETHRARGASNGLY
4   ASPASPARGTHRVALTHRTHRCYSALAGLU
5   GLUGLNTHRARGCYSLEUPHEVALGLNLEU
6   PROTYRSERGLUILEGLNGLUCYSLYSTHR
7   VALGLNGLNCYSALAGLUVALLEUGLUGLU
8   VALTHRALAILEGLYTYRPROALALYSCYS
9   CYSCYSGLUASPLEUCYSASNARGSERGLU
10   GLN

Samples:

sample_1: Prod1, [U-15N], 1 mM; sodium phosphate 50 mM; sodium chloride 150 mM; EDTA 1 mM; H2O 90%; D2O 10%

sample_2: Prod1, [U-13C; U-15N], 1 mM; sodium phosphate 50 mM; sodium chloride 150 mM; EDTA 1 mM; H2O 90%; D2O 10%

sample_3: Prod1, [U-13C; U-15N], 1 mM; sodium phosphate 50 mM; sodium chloride 150 mM; EDTA 1 mM; D2O 100%

sample_conditions_1: ionic strength: 0.2 M; pH: 6.5; 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 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1
3D 1H-13C aromatic NOESYsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
3D HN(CA)COsample_2isotropicsample_conditions_1
3D HA(CA)NHsample_2isotropicsample_conditions_1
3D HN(CACO)NHsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
3D HCCH-COSYsample_3isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1

Software:

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

ANSIG, Kraulis - data analysis

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMR spectrometers:

  • Varian INOVA 800 MHz
  • Varian INOVA 600 MHz
  • Varian INOVA 600 MHz
  • Varian UnityPlus 500 MHz

Related Database Links:

PDB
GB ABV29331

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