BMRB Entry 18834

Name: trans form of a photoswitchable PDZ domain crosslinked with an azobenzene derivative
Published: 2013-07-01

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PDB ID: 2m10
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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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

trans form of a photoswitchable PDZ domain crosslinked with an azobenzene derivative

Deposition date:

2012-11-09

Original release date:

2013-07-01

Authors:

Walser, Reto

Citation:

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).
PubMed: 23818626

Assembly members:

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:

Natural source: Common Name: Humans Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET30a(+)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PDZ: GPKPGDIFEVELAKNDNSLG ICVTGGVNTSVRHGGIYVKA VIPQGAAESDGRIHKGDRVL AVNGVSLEGATHKQAVCTLR NTGQVVHLLLEKGQSPT

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	391
15N chemical shifts	87
1H chemical shifts	628

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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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

VAL

ASN

THR

SER

4

VAL

ARG

HIS

GLY

ILE

TYR

VAL

LYS

ALA

5

VAL

ILE

PRO

GLN

GLY

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

HIS

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