BMRB Entry 17398
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17398
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Title: A protein from yeast PubMed: 22150589
Deposition date: 2011-01-07 Original release date: 2011-12-20
Authors: Qiu, Yu; Zhang, Jiahai; Zhang, Wen
Citation: Qiu, Yu; Zhang, Wen; Zhao, Chen; Wang, Yan; Wang, Weiwei; Zhang, Jiahai; Zhang, Zhiyong; Li, Guohong; Shi, Yunyu; Tu, Xiaoming; Wu, Jihui. "Solution structure of the Pdp1 PWWP domain reveals its unique binding sites for methylated H4K20 and DNA." Biochem. J. 442, 527-538 (2012).
Assembly members:
A protein from fission yeast, polymer, 216 residues, 24872.488 Da.
Natural source: Common Name: fission yeast Taxonomy ID: 4896 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Schizosaccharomyces pombe
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
A protein from fission yeast: SADDRLNFGDRILVKAPGYP
WWPALLLRRKETKDSLNTNS
SFNVLYKVLFFPDFNFAWVK
RNSVKPLLDSEIAKFLGSSK
RKSKELIEAYEASKTPPDLK
EESSTDLESADDRLNFGDRI
LVKAPGYPWWPALLLRRKET
KDSLNTNSSFNVLYKVLFFP
DFNFAWVKRNSVKPLLDSEI
AKFLGSSKRKSKELIEAYEA
SKTPPDLKEESSTDLE
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 379 |
| 15N chemical shifts | 105 |
| 1H chemical shifts | 661 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | A protein from fission yeast | 1 |
Entities:
Entity 1, A protein from fission yeast 216 residues - 24872.488 Da.
| 1 | SER | ALA | ASP | ASP | ARG | LEU | ASN | PHE | GLY | ASP | ||||
| 2 | ARG | ILE | LEU | VAL | LYS | ALA | PRO | GLY | TYR | PRO | ||||
| 3 | TRP | TRP | PRO | ALA | LEU | LEU | LEU | ARG | ARG | LYS | ||||
| 4 | GLU | THR | LYS | ASP | SER | LEU | ASN | THR | ASN | SER | ||||
| 5 | SER | PHE | ASN | VAL | LEU | TYR | LYS | VAL | LEU | PHE | ||||
| 6 | PHE | PRO | ASP | PHE | ASN | PHE | ALA | TRP | VAL | LYS | ||||
| 7 | ARG | ASN | SER | VAL | LYS | PRO | LEU | LEU | ASP | SER | ||||
| 8 | GLU | ILE | ALA | LYS | PHE | LEU | GLY | SER | SER | LYS | ||||
| 9 | ARG | LYS | SER | LYS | GLU | LEU | ILE | GLU | ALA | TYR | ||||
| 10 | GLU | ALA | SER | LYS | THR | PRO | PRO | ASP | LEU | LYS | ||||
| 11 | GLU | GLU | SER | SER | THR | ASP | LEU | GLU | SER | ALA | ||||
| 12 | ASP | ASP | ARG | LEU | ASN | PHE | GLY | ASP | ARG | ILE | ||||
| 13 | LEU | VAL | LYS | ALA | PRO | GLY | TYR | PRO | TRP | TRP | ||||
| 14 | PRO | ALA | LEU | LEU | LEU | ARG | ARG | LYS | GLU | THR | ||||
| 15 | LYS | ASP | SER | LEU | ASN | THR | ASN | SER | SER | PHE | ||||
| 16 | ASN | VAL | LEU | TYR | LYS | VAL | LEU | PHE | PHE | PRO | ||||
| 17 | ASP | PHE | ASN | PHE | ALA | TRP | VAL | LYS | ARG | ASN | ||||
| 18 | SER | VAL | LYS | PRO | LEU | LEU | ASP | SER | GLU | ILE | ||||
| 19 | ALA | LYS | PHE | LEU | GLY | SER | SER | LYS | ARG | LYS | ||||
| 20 | SER | LYS | GLU | LEU | ILE | GLU | ALA | TYR | GLU | ALA | ||||
| 21 | SER | LYS | THR | PRO | PRO | ASP | LEU | LYS | GLU | GLU | ||||
| 22 | SER | SER | THR | ASP | LEU | GLU |
Samples:
sample_1: a protein from fission yeast 0.6 mM; sodium phosphate 20 mM; sodium chloride 100 mM; EDTA 2 mM; H2O 90%; D2O 10%
sample_2: a protein from fission yeast 0.6 mM; sodium phosphate 20 mM; sodium chloride 100 mM; EDTA 2 mM; D2O 100%
sample_conditions_1: ionic strength: 0.140 M; pH: 4.8; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D C(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 HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_1 |
Software:
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
NMR spectrometers:
- Bruker DMX 600 MHz
Related Database Links:
| PDB |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts