BMRB Entry 19913
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19913
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Title: NMR Structure of KDM5B PHD1 finger PubMed: 24952722
Deposition date: 2014-04-16 Original release date: 2014-08-04
Authors: Zhang, Y.; Yang, H.; Guo, X.; Rong, N.; Song, Y.; Xu, Y.; Lan, W.; Xu, Y.; Cao, C.
Citation: Zhang, Y.; Yang, H.; Guo, X.; Rong, N.; Song, Y.; Xu, Y.; Lan, W.; Xu, Y.; Cao, C.. "The PHD1 finger of KDM5B recognizes unmodified H3K4 during the demethylation of histone H3K4me2/3 by KDM5B" Protein Cell ., .-. (2014).
Assembly members:
PHD1_finger_of_KDM5B, polymer, 55 residues, 6133.026 Da.
ZINC ION, non-polymer, 65.409 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):
PHD1_finger_of_KDM5B: AVDLYVCLLCGSGNDEDRLL
LCDGCDDSYHTFCLIPPLHD
VPKGDWRCPKCLAQE
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 189 |
| 15N chemical shifts | 51 |
| 1H chemical shifts | 301 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | PHD1 finger of KDM5B | 1 |
| 2 | ZINC ION_1 | 2 |
| 3 | ZINC ION_2 | 2 |
Entities:
Entity 1, PHD1 finger of KDM5B 55 residues - 6133.026 Da.
| 1 | ALA | VAL | ASP | LEU | TYR | VAL | CYS | LEU | LEU | CYS | ||||
| 2 | GLY | SER | GLY | ASN | ASP | GLU | ASP | ARG | LEU | LEU | ||||
| 3 | LEU | CYS | ASP | GLY | CYS | ASP | ASP | SER | TYR | HIS | ||||
| 4 | THR | PHE | CYS | LEU | ILE | PRO | PRO | LEU | HIS | ASP | ||||
| 5 | VAL | PRO | LYS | GLY | ASP | TRP | ARG | CYS | PRO | LYS | ||||
| 6 | CYS | LEU | ALA | GLN | GLU |
Entity 2, ZINC ION_1 - Zn - 65.409 Da.
| 1 | ZN |
Samples:
sample_1: PHD1 finger of KDM5B, [U-13C; U-15N], 0.8 mM; Phosphate buffer 50 mM; D2O 10%; H2O 90%
sample_2: PHD1 finger of KDM5B, [U-13C; U-15N], 0.8 mM; Phosphate buffer 50 mM; D2O 100%
sample_conditions_1: ionic strength: 100 mM; pH: 7.2; pressure: 1 atm; temperature: 293 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D_15N-separated_NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_2 | isotropic | sample_conditions_1 |
Software:
CNS, Brunger A. T. et.al. - refinement
NMR spectrometers:
- Agilent DD2 600 MHz
Related Database Links:
| BMRB | 19914 |
| PDB | |
| DBJ | BAC30898 BAD90482 BAE37363 BAE89761 BAG53706 |
| EMBL | CAB43532 CAB61368 CAB63108 CAH65222 |
| GB | AAD16061 AAH48180 AAH57318 AAI56050 AAI57032 |
| REF | NP_001026200 NP_001100647 NP_001300971 NP_006609 NP_690855 |
| SP | Q5F3R2 Q80Y84 Q9UGL1 |
| TPG | DAA21261 |
Download simulated HSQC data in one of the following formats:
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