BMRB Entry 17494
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17494
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Title: Zinc knuckle in PRDM4 PubMed: 21604305
Deposition date: 2011-02-26 Original release date: 2011-06-01
Authors: Briknarova, Klara; Atwater, Daniel; Glicken, Jessica; Maynard, Stacy; Ness, Tara
Citation: Briknarova, Klara; Atwater, Daniel; Glicken, Jessica; Maynard, Stacy; Ness, Tara. "The PR/SET domain in PRDM4 is preceded by a zinc knuckle." Proteins 79, 2341-2345 (2011).
Assembly members:
PRDM4(366-402), polymer, 39 residues, 4316.912 Da.
ZN, 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):
PRDM4(366-402): GSKENMATLFTIWCTLCDRA
YPSDCPEHGPVTFVPDTPI
- assigned_chemical_shifts
| Data type | Count |
| 15N chemical shifts | 36 |
| 1H chemical shifts | 258 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | PRDM4(366-402) | 1 |
| 2 | ZINC ION | 2 |
Entities:
Entity 1, PRDM4(366-402) 39 residues - 4316.912 Da.
G364 and S365 are cloning artefacts
| 1 | GLY | SER | LYS | GLU | ASN | MET | ALA | THR | LEU | PHE | ||||
| 2 | THR | ILE | TRP | CYS | THR | LEU | CYS | ASP | ARG | ALA | ||||
| 3 | TYR | PRO | SER | ASP | CYS | PRO | GLU | HIS | GLY | PRO | ||||
| 4 | VAL | THR | PHE | VAL | PRO | ASP | THR | PRO | ILE |
Entity 2, ZINC ION - Zn - 65.409 Da.
| 1 | ZN |
Samples:
H2O_sample: PRDM4(366-402) 0.5 mM; ZINC ION 2.5 mM; H2O 90%; D2O 10%; d11-Tris 50 mM; d16-TCEP 2.5 mM
D2O_sample: PRDM4(366-402) 0.5 mM; ZINC ION 2.5 mM; D2O 100%; d11-Tris 50 mM; d16-TCEP 2.5 mM
15N_sample: PRDM4(366-402), [U-100% 15N], 0.25 mM; ZINC ION 1.6 mM; H2O 90%; D2O 10%; d11-Tris 50 mM; d16-TCEP 2.5 mM
sample_conditions_1: pH: 7.15; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D DQF-COSY | H2O_sample | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | H2O_sample | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | H2O_sample | isotropic | sample_conditions_1 |
| ECOSY | D2O_sample | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | 15N_sample | isotropic | sample_conditions_1 |
| 3D HNHA | 15N_sample | isotropic | sample_conditions_1 |
| 3D HNHB | 15N_sample | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | 15N_sample | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | 15N_sample | isotropic | sample_conditions_1 |
| 2D 1H-15N HMQC | 15N_sample | isotropic | sample_conditions_1 |
Software:
VNMRJ, Varian - collection
FELIX, Felix NMR Inc. - chemical shift assignment, data analysis, processing
ARIA v2.3, Linge, O, . - refinement, structure solution
NMR spectrometers:
- Varian Uniform NMR System 600 MHz
Related Database Links:
| PDB | |
| DBJ | BAG10863 BAG51692 |
| EMBL | CAB61401 CAH92945 |
| GB | AAD55249 AAH35581 ABM82163 ABM85348 AIC50813 |
| REF | NP_001126735 NP_001244489 NP_036538 XP_001162965 XP_002807184 |
| SP | Q5R5M1 Q9UKN5 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts