BMRB Entry 18834
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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/BMR18834
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Title: trans form of a photoswitchable PDZ domain crosslinked with an azobenzene derivative PubMed: 23818626
Deposition date: 2012-11-09 Original release date: 2013-07-01
Authors: Walser, Reto
Citation: Buchli, Brigitte; Waldauer, Steven; Walser, Reto; Donten, Mateusz; Pfister, Rolf; Blochliger, Nicolas; Steiner, Sandra; Caflisch, Amedeo; Zerbe, Oliver; Hamm, Peter. "Kinetic response of a photoperturbed allosteric protein." Proc. Natl. Acad. Sci. U.S.A. 110, 11725-11730 (2013).
Assembly members:
PDZ, polymer, 97 residues, 10067.491 Da.
3,3'-(E)-diazene-1,2-diylbis{6-[(chloroacetyl)amino]benzenesulfonic acid}, non-polymer, 525.340 Da.
Natural source: Common Name: Humans Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
PDZ: GPKPGDIFEVELAKNDNSLG
ICVTGGVNTSVRHGGIYVKA
VIPQGAAESDGRIHKGDRVL
AVNGVSLEGATHKQAVCTLR
NTGQVVHLLLEKGQSPT
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 391 |
| 15N chemical shifts | 87 |
| 1H chemical shifts | 628 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | PDZ | 1 |
| 2 | 33B | 2 |
Entities:
Entity 1, PDZ 97 residues - 10067.491 Da.
| 1 | GLY | PRO | LYS | PRO | GLY | ASP | ILE | PHE | GLU | VAL | ||||
| 2 | GLU | LEU | ALA | LYS | ASN | ASP | ASN | SER | LEU | GLY | ||||
| 3 | ILE | CYS | VAL | THR | GLY | GLY | VAL | ASN | THR | SER | ||||
| 4 | VAL | ARG | HIS | GLY | GLY | ILE | TYR | VAL | LYS | ALA | ||||
| 5 | VAL | ILE | PRO | GLN | GLY | ALA | ALA | GLU | SER | ASP | ||||
| 6 | GLY | ARG | ILE | HIS | LYS | GLY | ASP | ARG | VAL | LEU | ||||
| 7 | ALA | VAL | ASN | GLY | VAL | SER | LEU | GLU | GLY | ALA | ||||
| 8 | THR | HIS | LYS | GLN | ALA | VAL | CYS | THR | LEU | ARG | ||||
| 9 | ASN | THR | GLY | GLN | VAL | VAL | HIS | LEU | LEU | LEU | ||||
| 10 | GLU | LYS | GLY | GLN | SER | PRO | THR |
Entity 2, 33B - C16 H14 Cl2 N4 O8 S2 - 525.340 Da.
| 1 | 33B |
Samples:
sample_3: PDZ, [U-100% 15N], 0.75 mM; sodium phosphate 50 mM; sodium chloride 150 mM; sodium azide 0.1 mM; C12E5 4.3%; n-hexanol 1.8%; H2O 90%; D2O 10%
sample_2: PDZ, [U-100% 15N], 0.75 mM; sodium phosphate 50 mM; sodium chloride 150 mM; sodium azide 0.1 mM; Pf1 phage 8.5 mg/mL; H2O 90%; D2O 10%
sample_1: PDZ, [U-99% 13C; U-99% 15N], 0.75 mM; sodium phosphate 50 mM; sodium chloride 150 mM; sodium azide 0.1 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 0.2 M; pH: 6.8; pressure: 1 atm; temperature: 298 K
sample_conditions_2: ionic strength: 0.2 M; pH: 6.8; pressure: 1 atm; temperature: 298 K
sample_conditions_3: ionic strength: 0.2 M; pH: 6.8; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | 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 CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | anisotropic | sample_conditions_2 |
| 2D 1H-15N HSQC | sample_3 | anisotropic | sample_conditions_3 |
Software:
TOPSPIN v2.1, Bruker Biospin - collection, processing
CARA v1.9.0b3, Keller and Wuthrich - chemical shift assignment
TALOS v3.80F1 Rev 2012.080.14.41, Cornilescu, Delaglio and Bax - data analysis
CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution
X-PLOR NIH v2.32, Schwieters, Kuszewski, Tjandra and Clore - refinement
ProcheckNMR, Laskowski and MacArthur - data analysis
WhatIF, Vriend - data analysis
NMR spectrometers:
- Bruker Avance 600 MHz
- Bruker Avance 700 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts