BMRB Entry 25221

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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/BMR25221
MolProbity Validation Chart

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Title:
Solution structure of the PHD domain of Yeast YNG2
Deposition date:
2014-09-12
Original release date:
2014-12-22
Authors:
Taeb, Samira; Kaustov, Lilia; Lemak, Alexander; Farhadi, Sahar; Sheng, Yi
Citation:

Citation: Taeb, Samira; Kaustov, Lilia; Lemak, Alexander; Farhadi, Sahar; Sheng, Yi. "Solution structure of the PHD domain of Yeast YNG2"  .

Assembly members:

Assembly members:
entity_1, polymer, 50 residues, 5938.856 Da.
ZINC ION, non-polymer, 65.409 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: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: TLYCFCQRVSFGEMVACDGP NCKYEWFHYDCVNLKEPPKG TWYCPECKIE

Data sets:
Data typeCount
1H chemical shifts340
13C chemical shifts213
15N chemical shifts49

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_11
2ZINC ION_12
3ZINC ION_22

Entities:

Entity 1, entity_1 50 residues - 5938.856 Da.

1   THRLEUTYRCYSPHECYSGLNARGVALSER
2   PHEGLYGLUMETVALALACYSASPGLYPRO
3   ASNCYSLYSTYRGLUTRPPHEHISTYRASP
4   CYSVALASNLEULYSGLUPROPROLYSGLY
5   THRTRPTYRCYSPROGLUCYSLYSILEGLU

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: entity_1, [U-13C; U-15N], 0.5 mM; sodium chloride 300 mM; potassium chloride 2.7 mM; potassium phosphate 2 mM; sodium phosphate 10 mM; CHAPS 0.05 mM; H2O 90%; D2O 10%

sample_conditions_1: temperature: 273 K; pH: 6.5; pressure: 1 atm; ionic strength: 300 mM

Experiments:

NameSampleSample stateSample conditions
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

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

SPARKY, Goddard - peak picking

FMCGUI, Lemak A., Gutmanas A., Chitayat S., Karra M., Far s C., Sunnerhagen M., and Arrowsmith CH - chemical shift assignment, refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

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

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

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

DBJ GAA23808
EMBL CAY80101
GB AAB68930 AHY77791 AJP39190 AJU16386 AJU16646
REF NP_011958
SP P38806
TPG DAA06786
AlphaFold P38806

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