BMRB Entry 16879

Name: Chemical shift assignments of the 3rd PDZ domain of protein tyrosine phosphatase basophil like (PTP-BL)
Published: 2010-07-27

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PDB ID: 6gbd
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16879
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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:

Chemical shift assignments of the 3rd PDZ domain of protein tyrosine phosphatase basophil like (PTP-BL)

Deposition date:

2010-04-19

Original release date:

2010-07-27

Authors:

Kock, Gerd; Dicks, Markus; Stoll, Raphael

Citation:

Citation: Kock, Gerd; Dicks, Markus; Heumann, Rolf; Erdmann, Kai; Stoll, Raphael. "Sequence-specific 1H, 13C, and 15N assignment of the extended PDZ3 domain of the protein tyrosine phosphatase basophil-like PTP-BL." Biomol. NMR Assignments 4, 199-202 (2010).
PubMed: 20563762

Assembly members:

Assembly members:
PDZ3_PTP-BL, polymer, 119 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGex-2T

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PDZ3_PTP-BL: TPHVKDYSFVTEDNTFEVKL FKNSSGLGFSFSREDNLIPE QINGSIVRVKKLFPGQPAAE SGKIDVGDVILKVNGAPLKG LSQQDVISALRGTAPEVSLL LCRPAPGVLPEIDTPGNSS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	384
15N chemical shifts	100
1H chemical shifts	617

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PDZ3 domain	1

Entities:

Entity 1, PDZ3 domain 119 residues - Formula weight is not available

According to the UniProt Database, the coding sequence of PDZ3 of PTP-BL comprises residues Glu17 to Ala105

1

THR

PRO

HIS

VAL

LYS

ASP

TYR

SER

PHE

VAL

2

THR

GLU

ASP

ASN

THR

PHE

GLU

VAL

LYS

LEU

3

PHE

LYS

ASN

SER

GLY

LEU

GLY

PHE

SER

4

PHE

SER

ARG

GLU

ASP

ASN

LEU

ILE

PRO

GLU

5

GLN

ILE

ASN

GLY

SER

ILE

VAL

ARG

VAL

LYS

6

LYS

LEU

PHE

PRO

GLY

GLN

PRO

ALA

GLU

7

SER

GLY

LYS

ILE

ASP

VAL

GLY

ASP

VAL

ILE

8

LEU

LYS

VAL

ASN

GLY

ALA

PRO

LEU

LYS

GLY

9

LEU

SER

GLN

ASP

VAL

ILE

SER

ALA

LEU

10

ARG

GLY

THR

ALA

PRO

GLU

VAL

SER

LEU

11

LEU

CYS

ARG

PRO

ALA

PRO

GLY

VAL

LEU

PRO

12

GLU

ILE

ASP

THR

PRO

GLY

ASN

SER

Samples:

sample_1: PDZ3, [U-15N], 0.5 – 1.0 mM; TSP 1.0 mM; H2O 90%; D2O 10%; potassium phosphate 1.4 mM; potassium chloride 2.7 mM; sodium chloride 137 mM; sodium phosphate 9 mM

sample_2: PDZ3, [U-100% 13C; U-100% 15N], 0.5 – 1.0 mM; TSP 1.0 mM; H2O 90%; D2O 10%; potassium phosphate 1.4 mM; potassium chloride 2.7 mM; sodium chloride 137 mM; sodium phosphate 9 mM

sample_conditions_1: ionic strength: 0.15 M; pH: 7.4; 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	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNHA	sample_2	isotropic	sample_conditions_1
3D HNHB	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1

Software:

NMRView v5.2.2, Johnson, One Moon Scientific - data analysis, peak picking

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMR spectrometers:

Bruker DRX 600 MHz