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
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Title: 1H, 13C, 15N chemical shift assignments of Dido PHD domain PubMed: 23579637
Deposition date: 2013-01-19 Original release date: 2013-08-05
Authors: Santiveri, Clara; Perez-Canadillas, Jose; Jimenez, M Angeles
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).
Assembly members:
Dido_PHD, polymer, 61 residues, 7048.059 Da.
ZINC ION, non-polymer, 65.409 Da.
Natural source: Common Name: Humans Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Dido_PHD: GSMDPNALYCICRQPHNNRF
MICCDRCEEWFHGDCVGISE
ARGRLLERNGEDYICPNCTI
L
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 268 |
| 15N chemical shifts | 68 |
| 1H chemical shifts | 808 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Dido_PHD | 1 |
| 2 | ZINC ION_1 | 2 |
| 3 | ZINC ION_2 | 2 |
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 | GLY | SER | MET | ASP | PRO | ASN | ALA | LEU | TYR | CYS | ||||
| 2 | ILE | CYS | ARG | GLN | PRO | HIS | ASN | ASN | ARG | PHE | ||||
| 3 | MET | ILE | CYS | CYS | ASP | ARG | CYS | GLU | GLU | TRP | ||||
| 4 | PHE | HIS | GLY | ASP | CYS | VAL | GLY | ILE | SER | GLU | ||||
| 5 | ALA | ARG | GLY | ARG | LEU | LEU | GLU | ARG | ASN | GLY | ||||
| 6 | GLU | ASP | TYR | ILE | CYS | PRO | ASN | CYS | THR | ILE | ||||
| 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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HNHA | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_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 |