BMRB Entry 18963

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18963
MolProbity Validation Chart

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Title:
1H, 13C, 15N chemical shift assignments of Dido PHD domain
Deposition date:
2013-01-19
Original release date:
2013-08-05
Authors:
Santiveri, Clara; Perez-Canadillas, Jose; Jimenez, M Angeles
Citation:

Citation: Santiveri, Clara; Garcia-Mayoral, Maria; Perez-Canadillas, Jose; Jimenez, M Angeles. "NMR structure note: PHD domain from death inducer obliterator protein and its interaction with H3K4me3"  J. Biomol. NMR 56, 183-190 (2013).
PubMed: 23579637

Assembly members:

Assembly members:
Dido_PHD, polymer, 61 residues, 7048.059 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: pET28

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Dido_PHD: GSMDPNALYCICRQPHNNRF MICCDRCEEWFHGDCVGISE ARGRLLERNGEDYICPNCTI L

Data sets:
Data typeCount
13C chemical shifts268
15N chemical shifts68
1H chemical shifts808

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Dido_PHD1
2ZINC ION_12
3ZINC ION_22

Entities:

Entity 1, Dido_PHD 61 residues - 7048.059 Da.

Residues 1-3, GSM, are the cloning tag. Residues 4-61 correspond to residues 265-322 from human Dido or to residues 262-319 from mouse Dido.

1   GLYSERMETASPPROASNALALEUTYRCYS
2   ILECYSARGGLNPROHISASNASNARGPHE
3   METILECYSCYSASPARGCYSGLUGLUTRP
4   PHEHISGLYASPCYSVALGLYILESERGLU
5   ALAARGGLYARGLEULEUGLUARGASNGLY
6   GLUASPTYRILECYSPROASNCYSTHRILE
7   LEU

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: Dido_PHD 0.6 mM; potassium phosphate 10 uM; TCEP 100 uM; H2O 90%; D2O 10%; DSS 10 uM

sample_2: Dido_PHD, [U-99% 13C; U-99% 15N], 0.4 mM; potassium phosphate 10 uM; TCEP 100 uM; sodium azide 0.01%; H2O 90%; D2O 10%; DSS 10 uM

sample_conditions_1: ionic strength: 10 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1
3D HNHAsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment

TALOS, Cornilescu, Delaglio and Bax - dihedral angles

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

UNP Q9BTC0 Q8C9B9
BMRB 19074
PDB
DBJ BAA20791 BAA92094 BAC31270 BAC97927 BAE88140
EMBL CAB48401 CAG31367 CAH89967
GB AAH00770 AAH04237 AAH14489 AAH29110 AAH96662
REF NP_001124926 NP_001180298 NP_001180299 NP_001278361 NP_001278362
SP Q8C9B9 Q9BTC0
AlphaFold Q9UFB6 Q9WV00 Q8C9B9 Q9BTC0