BMRB Entry 19682
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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/BMR19682
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Title: Solution NMR Structure of PHD Type 1 Zinc Finger Domain 1 of Lysine-specific Demethylase Lid from Drosophila melanogaster, Northeast Structural Genomics Consortium (NESG) Target FR824J
Deposition date: 2013-12-13 Original release date: 2014-01-22
Authors: Xu, Xianzhong; Eletsky, Alexander; Lee, Dan; Kohan, Eitan; Janjua, Haleema; Xiao, Rong; Acton, Thomas; Everett, John; Sukumaran, Dinesh; Montelione, Gaetano; Szyperski, Thomas
Citation: Xu, Xianzhong; Eletsky, Alexander; Lee, Dan; Kohan, Eitan; Janjua, Haleema; Xiao, Rong; Acton, Thomas; Everett, John; Sukumaran, Dinesh; Montelione, Gaetano; Szyperski, Thomas. "Solution NMR Structure of PHD Type 1 Zinc Finger Domain 1 from Lysine-specific Demethylase Lid from Drosophila melanogaster, Northeast Structural Genomics Consortium (NESG) Target FR824J" To be published ., .-..
Assembly members:
FR824J, polymer, 94 residues, 10196.379 Da.
entity_ZN, non-polymer, 65.409 Da.
Natural source: Common Name: fruit fly Taxonomy ID: 7227 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Drosophila melanogaster
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
FR824J: SHMSGGSPLATGTTANTRGA
SQKKGGEPPALIVDPLMKYI
CHICNRGDVEESMLLCDGCD
DSYHTFCLLPPLTSIPKGEW
LCPRCVVEEVSKPQ
- assigned_chemical_shifts
- RDCs
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 392 |
| 15N chemical shifts | 95 |
| 1H chemical shifts | 628 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | FR824J | 1 |
| 2 | Zn-1 | 2 |
| 3 | Zn-2 | 2 |
Entities:
Entity 1, FR824J 94 residues - 10196.379 Da.
Residues 1-3 represent a non-native affinity tag remainder after his tag cleavage.
| 1 | SER | HIS | MET | SER | GLY | GLY | SER | PRO | LEU | ALA | ||||
| 2 | THR | GLY | THR | THR | ALA | ASN | THR | ARG | GLY | ALA | ||||
| 3 | SER | GLN | LYS | LYS | GLY | GLY | GLU | PRO | PRO | ALA | ||||
| 4 | LEU | ILE | VAL | ASP | PRO | LEU | MET | LYS | TYR | ILE | ||||
| 5 | CYS | HIS | ILE | CYS | ASN | ARG | GLY | ASP | VAL | GLU | ||||
| 6 | GLU | SER | MET | LEU | LEU | CYS | ASP | GLY | CYS | ASP | ||||
| 7 | ASP | SER | TYR | HIS | THR | PHE | CYS | LEU | LEU | PRO | ||||
| 8 | PRO | LEU | THR | SER | ILE | PRO | LYS | GLY | GLU | TRP | ||||
| 9 | LEU | CYS | PRO | ARG | CYS | VAL | VAL | GLU | GLU | VAL | ||||
| 10 | SER | LYS | PRO | GLN |
Entity 2, Zn-1 - Zn - 65.409 Da.
| 1 | ZN |
Samples:
FR824J.004: FR824J 0.321 mM
FR824J.003: FR824J 0.321 mM
sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | FR824J.003 | isotropic | sample_conditions_1 |
| 3D HNCO | FR824J.003 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | FR824J.003 | isotropic | sample_conditions_1 |
| 3D HNCACB | FR824J.003 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | FR824J.003 | isotropic | sample_conditions_1 |
| 3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY | FR824J.003 | isotropic | sample_conditions_1 |
| 2D 1H-13C ct HSQC aliphatic | FR824J.003 | isotropic | sample_conditions_1 |
| 2D 1H-13C ct HSQC aromatic | FR824J.003 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | FR824J.003 | isotropic | sample_conditions_1 |
| 3D (H)CCH-COSY-ali | FR824J.003 | isotropic | sample_conditions_1 |
| 3D (H)CCH-COSY aro | FR824J.003 | isotropic | sample_conditions_1 |
| 3D (H)CCH-TOCSY ali | FR824J.003 | isotropic | sample_conditions_1 |
| 2D gNfHSQC_His | FR824J.004 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | FR824J.004 | isotropic | sample_conditions_1 |
| 2D 1H-13C ct-HSQC(28ms) | FR824J.004 | isotropic | sample_conditions_1 |
| 2D 1H-13C ct- HSQC(42ms) | FR824J.004 | isotropic | sample_conditions_1 |
| 2D 1H-13C ct-HSQC(56ms) | FR824J.004 | isotropic | sample_conditions_1 |
| 2D J-modulation HSQC | FR824J.004 | isotropic | sample_conditions_1 |
Software:
CNS, Brunger, Adams, Clore, Gros, Nilges and Read, David Wishart,Leigh Willard,Tim Jellard,Brian Sykes, Guntert, Keller and Wuthrich - data analysis, processing, refinemen, structure solution, geometry optimization
CYANA v3.0, Guntert, Mumenthaler and Wuthrich - refinement, geometry optimization, structure solution
AutoStructure v2.1, Huang, Tejero, Powers and Montelione - data analysis, refinement
AutoAssign v2.1, Zimmerman, Moseley, Kulikowski and Montelione - data analysis, chemical shift assignment
XEASY, Bartels et al. - data analysis
VNMRJ, Varian - collection
TALOS+, Shen, Cornilescu, Delaglio and Bax - geometry optimization
PSVS, Bhattacharya, Montelione - structure validation
NMR spectrometers:
- Varian INOVA 750 MHz
- Varian INOVA 600 MHz
Related Database Links:
| UNP | Q9VMJ7 |
| PDB | |
| GB | AAF52319 AAM11379 AAN10569 AFH03582 AFH03583 |
| REF | NP_001245908 NP_001245909 NP_001245910 NP_001285649 NP_523486 |
| SP | Q9VMJ7 |
Download simulated HSQC data in one of the following formats:
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or all simulated shifts
SPARKY: Backbone
or all simulated shifts