BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 18834

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

Data sets:
Data typeCount
13C chemical shifts391
15N chemical shifts87
1H chemical shifts628

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1PDZ1
233B2

Entities:

Entity 1, PDZ 97 residues - 10067.491 Da.

1   GLYPROLYSPROGLYASPILEPHEGLUVAL
2   GLULEUALALYSASNASPASNSERLEUGLY
3   ILECYSVALTHRGLYGLYVALASNTHRSER
4   VALARGHISGLYGLYILETYRVALLYSALA
5   VALILEPROGLNGLYALAALAGLUSERASP
6   GLYARGILEHISLYSGLYASPARGVALLEU
7   ALAVALASNGLYVALSERLEUGLUGLYALA
8   THRHISLYSGLNALAVALCYSTHRLEUARG
9   ASNTHRGLYGLNVALVALHISLEULEULEU
10   GLULYSGLYGLNSERPROTHR

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2anisotropicsample_conditions_2
2D 1H-15N HSQCsample_3anisotropicsample_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

Related Database Links:

BMRB 18833 4123 4124 4516
PDB

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts