BMRB Entry 11469
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11469
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Title: Solution structure of the plant homeodomain (PHD) of the E3 SUMO ligase Siz1 from rice PubMed: 22626555
Deposition date: 2012-01-11 Original release date: 2012-08-13
Authors: Shindo, Heisaburo; Tsuchiya, Wataru; Suzuki, Rintaro; Yamazaki, Toshimasa
Citation: Shindo, Heisaburo; Suzuki, Rintaro; Tsuchiya, Wataru; Taichi, Misako; Nishiuchi, Yuji; Yamazaki, Toshimasa. "PHD finger of the SUMO ligase Siz/PIAS family in rice reveals specific binding for methylated histone H3 at lysine 4 and arginine 2" FEBS Lett. 586, 1783-1789 (2012).
Assembly members:
entity_1, polymer, 68 residues, 7671.758 Da.
ZINC ION, non-polymer, 65.409 Da.
Natural source: Common Name: Oryza sativa subsp. japonica Taxonomy ID: 39947 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Oryza Oryza sativa
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity_1: GSDSFQPEAKVRCICSSTMV
NDSMIQCEDQRCQVWQHLNC
VLIPDKPGESAEVPPVFYCE
LCRLSRAD
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 308 |
| 15N chemical shifts | 72 |
| 1H chemical shifts | 460 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | ZINC ION_1 | 2 |
| 3 | ZINC ION_2 | 2 |
Entities:
Entity 1, entity_1 68 residues - 7671.758 Da.
Residues 105-106 represent a non-native sequence from affinity tag.
| 1 | GLY | SER | ASP | SER | PHE | GLN | PRO | GLU | ALA | LYS | ||||
| 2 | VAL | ARG | CYS | ILE | CYS | SER | SER | THR | MET | VAL | ||||
| 3 | ASN | ASP | SER | MET | ILE | GLN | CYS | GLU | ASP | GLN | ||||
| 4 | ARG | CYS | GLN | VAL | TRP | GLN | HIS | LEU | ASN | CYS | ||||
| 5 | VAL | LEU | ILE | PRO | ASP | LYS | PRO | GLY | GLU | SER | ||||
| 6 | ALA | GLU | VAL | PRO | PRO | VAL | PHE | TYR | CYS | GLU | ||||
| 7 | LEU | CYS | ARG | LEU | SER | ARG | ALA | ASP |
Entity 2, ZINC ION_1 - Zn - 65.409 Da.
| 1 | ZN |
Samples:
sample_1: OsSiz1-PHD, [U-13C; U-15N], 0.5 – 1.0 mM; ZINC ION1.0 – 2.0 mM; sodium chloride 100 mM; potassium phosphate 10 mM; DTT 5 mM; H2O 92%; D2O 8%
sample_2: OsSiz1-PHD, [U-13C; U-15N], 0.5 – 1.0 mM; ZINC ION1.0 – 2.0 mM; sodium chloride 100 mM; potassium phosphate 10 mM; DTT 5 mM; D2O 100%
sample_conditions_1: pH: 7.0; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HCABGCO | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | sample_2 | isotropic | sample_conditions_1 |
| 3D 15N-separated NOESY-HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D 13C/15N-separated NOESY-HSQC | sample_1 | isotropic | sample_conditions_1 |
| 4D 13C/13C-separated NOESY-HSQC | sample_2 | isotropic | sample_conditions_1 |
Software:
xwinnmr v3.1, Bruker Biospin - collection
NMRPipe vreleased at Feb 10, 2006, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY v3.113, Goddard - chemical shift assignment, peak picking
CYANA v2.1, Guntert, Mumenthaler and Wuthrich - refinement, structure solution
TALOS+ v1.01F, Shen, Delaglio, Cornilescu and Bax - data analysis
AQUA v3.2, Rullmann, Doreleijers and Kaptein - data analysis
ProcheckNMR v3.5.4, Laskowski and MacArthur - data analysis
NMR spectrometers:
- Bruker DMX 750 MHz
Related Database Links:
| PDB | |
| DBJ | BAF16431 BAG97182 BAS92058 |
| GB | AAT39226 EEC78434 EEE62174 |
| REF | NP_001054517 |
| SP | Q6L4L4 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts