BMRB Entry 25562
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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/BMR25562
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Title: Structure of the PR domain from PRDM16
Deposition date: 2015-04-02 Original release date: 2016-07-05
Authors: Sun, Yizhi; Armstrong, Geoffrey; Briknarova, Klara
Citation: Sun, Yizhi; Armstrong, Geoffrey; Briknarova, Klara. "Structure of the PR Domain from PRDM16" Not known ., .-..
Assembly members:
entity, polymer, 176 residues, 19169.670 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity: GSGFPTSEDFTPKEGSPYEA
PVYIPEDIPIPADFELRESS
IPGAGLGVWAKRKMEAGERL
GPCVVVPRAAAKETDFGWEQ
ILTDVEVSPQEGCITKISED
LGSEKFCVDANQAGAGSWLK
YIRVACSCDDQNLTMCQISE
QIYYKVIKDIEPGEELLVHV
KEGVYPLGTVPPGLDE
- assigned_chemical_shifts
Data type | Count |
13C chemical shifts | 737 |
15N chemical shifts | 168 |
1H chemical shifts | 1160 |
Additional metadata:
Assembly:
Entity Assembly ID | Entity Name | Entity ID |
---|---|---|
1 | entity | 1 |
Entities:
Entity 1, entity 176 residues - 19169.670 Da.
The recombinant protein contains three extraneous amino acids at the N-terminus and residues 54-226 of human MEL1 (gsgFPTS...GLDE).
1 | GLY | SER | GLY | PHE | PRO | THR | SER | GLU | ASP | PHE | ||||
2 | THR | PRO | LYS | GLU | GLY | SER | PRO | TYR | GLU | ALA | ||||
3 | PRO | VAL | TYR | ILE | PRO | GLU | ASP | ILE | PRO | ILE | ||||
4 | PRO | ALA | ASP | PHE | GLU | LEU | ARG | GLU | SER | SER | ||||
5 | ILE | PRO | GLY | ALA | GLY | LEU | GLY | VAL | TRP | ALA | ||||
6 | LYS | ARG | LYS | MET | GLU | ALA | GLY | GLU | ARG | LEU | ||||
7 | GLY | PRO | CYS | VAL | VAL | VAL | PRO | ARG | ALA | ALA | ||||
8 | ALA | LYS | GLU | THR | ASP | PHE | GLY | TRP | GLU | GLN | ||||
9 | ILE | LEU | THR | ASP | VAL | GLU | VAL | SER | PRO | GLN | ||||
10 | GLU | GLY | CYS | ILE | THR | LYS | ILE | SER | GLU | ASP | ||||
11 | LEU | GLY | SER | GLU | LYS | PHE | CYS | VAL | ASP | ALA | ||||
12 | ASN | GLN | ALA | GLY | ALA | GLY | SER | TRP | LEU | LYS | ||||
13 | TYR | ILE | ARG | VAL | ALA | CYS | SER | CYS | ASP | ASP | ||||
14 | GLN | ASN | LEU | THR | MET | CYS | GLN | ILE | SER | GLU | ||||
15 | GLN | ILE | TYR | TYR | LYS | VAL | ILE | LYS | ASP | ILE | ||||
16 | GLU | PRO | GLY | GLU | GLU | LEU | LEU | VAL | HIS | VAL | ||||
17 | LYS | GLU | GLY | VAL | TYR | PRO | LEU | GLY | THR | VAL | ||||
18 | PRO | PRO | GLY | LEU | ASP | GLU |
Samples:
sample_1: entity, [U-99% 13C; U-99% 15N], 0.45-0.55 mM; potassium phosphate 20 mM; potassium chloride 50 mM; DTT 2.5 mM; H2O 90%; D2O 10%
sample_2: entity, [U-99% 15N], 0.4-0.5 mM; potassium phosphate 20 mM; potassium chloride 50 mM; DTT 2.5 mM; H2O 90%; D2O 10%
sample_3: entity 0.5 mM; potassium phosphate 20 mM; potassium chloride 50 mM; DTT 2.5 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 0.088 M; pH: 6.8; pressure: 1 atm; temperature: 298 K
Experiments:
Name | Sample | Sample state | Sample conditions |
---|---|---|---|
2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
3D HNCACB | 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 HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
3D CCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
2D HBCB(CGCD)HD | sample_1 | isotropic | sample_conditions_1 |
3D 1H-15N NOESY | sample_2 | isotropic | sample_conditions_1 |
2D DQF-COSY | sample_3 | isotropic | sample_conditions_1 |
2D 1H-1H TOCSY | sample_3 | isotropic | sample_conditions_1 |
Software:
VNMRJ, Agilent - collection
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
CcpNmr, CCPN - chemical shift assignment, data analysis, peak picking
ARIA, Linge, O'Donoghue and Nilges - refinement, structure solution
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution
TALOS, Cornilescu, Delaglio and Bax - generation of torsion angle restraints
NMR spectrometers:
- Varian Varian NMR System 800 MHz
- Varian Varian NMR System 900 MHz
- Varian Varian NMR System 500 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts