BMRB Entry 11248

Name: Solution structure of the PDZ domain from mouse LIM domain kinase
Published: 2011-08-03

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PDB ID: 2yub
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11248
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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:

Solution structure of the PDZ domain from mouse LIM domain kinase

Deposition date:

2010-07-23

Original release date:

2011-08-03

Authors:

Hayashi, F.; Suetake, T.; Yokoyama, S.

Citation:

Citation: Hayashi, F.; Suetake, T.; Yokoyama, S.. "Solution structure of the PDZ domain from mouse LIM domain kinase" .

Assembly members:

Assembly members:
PDZ domain, polymer, 118 residues, Formula weight is not available

Natural source:

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

Experimental source:

Experimental source: Production method: cell free synthesis Host organism: E. coli - cell free Vector: P041220-03

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PDZ domain: GSSGSSGVQDQLPYSVTLIS MPATTECRRGFSVTVESASS NYATTVQVKEVNRMHISPNN RNAIHPGDRILEINGTPVRT LRVEEVEDAIKQTSQTLQLL IEHDPVPQRLDQSGPSSG

Data sets:

assigned_chemical_shifts
- chemical_shift_1

Data type	Count
13C chemical shifts	483
15N chemical shifts	115
1H chemical shifts	782

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PDZ domain	1

Entities:

Entity 1, PDZ domain 118 residues - Formula weight is not available

1

GLY

SER

GLY

SER

GLY

VAL

GLN

ASP

2

GLN

LEU

PRO

TYR

SER

VAL

THR

LEU

ILE

SER

3

MET

PRO

ALA

THR

GLU

CYS

ARG

GLY

4

PHE

SER

VAL

THR

VAL

GLU

SER

ALA

SER

5

ASN

TYR

ALA

THR

VAL

GLN

VAL

LYS

GLU

6

VAL

ASN

ARG

MET

HIS

ILE

SER

PRO

ASN

7

ARG

ASN

ALA

ILE

HIS

PRO

GLY

ASP

ARG

ILE

8

LEU

GLU

ILE

ASN

GLY

THR

PRO

VAL

ARG

THR

9

LEU

ARG

VAL

GLU

VAL

GLU

ASP

ALA

ILE

10

LYS

GLN

THR

SER

GLN

THR

LEU

GLN

LEU

11

ILE

GLU

HIS

ASP

PRO

VAL

PRO

GLN

ARG

LEU

12

ASP

GLN

SER

GLY

PRO

SER

GLY

Samples:

sample_1: PDZ domain, [U-13C; U-15N], 0.47 mM; d-Tris-HCl 20 mM; NaCl 100 mM; d-DTT 1 mM; NaN3 0.02%; H2O 90%; D2O 10%

condition_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 13C-separated NOESY	sample_1	isotropic	condition_1
3D 15N-separated NOESY	sample_1	isotropic	condition_1

Software:

VNMR v6.1C, Varian - collection

NMRPipe v20031121, Delaglio, F. - processing

NMRView v5.0.4, Johnson, B.A. - data analysis

Kujira v0.9820, Kobayashi, N. - data analysis

CYANA v2.1, Guntert, P. - refinement, structure solution

NMR spectrometers:

Varian INOVA 800 MHz

PDB	2YUB
DBJ	BAA06675 BAA24488 BAA24489 BAA24491 BAA29035
GB	AAC39947 AAH07129 ABK42255 EDL40412 EDL40413
REF	NP_001029202 NP_034848 NP_774958 XP_005366157 XP_006514610
SP	O54785
AlphaFold	O54785