BMRB Entry 6060

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PDB ID: 1gm1
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR6060
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

1H, 13C, and 15N Chemical Shift Assignments for a complex of PDZ2 from PTP-BL with the C-terminus of APC (adenomatous polyposis coli)

Deposition date:

2004-01-06

Original release date:

2011-08-11

Authors:

Walma, Tine; Vuister, Geerten

Citation:

Citation: Walma, Tine; Aelen, J.; Nabuurs, S.; Oostendorp, M.; van den Berk, L.; Hendriks, W.; Vuister, Geerten. "A closed binding pocket and global destabilization modify the binding properties of an alternatively spliced form of the second PDZ domain of PTP-BL" Structure 12, 11-20 (2004).
PubMed: 14725761

Assembly members:

Assembly members:
Second PDZ domain from PTP-BL, polymer, 102 residues, 9752.07 Da.
C-terminus from APC, polymer, 12 residues, 1333.51 Da.

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: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Second PDZ domain from PTP-BL: MHHHHHHMKPGDTFEVELAK TDGSLGISVTGGVNTSVRHG GIYVKAIIPKGAAESDGRIH KGDRVLAVNGVSLEGATHKQ AVETLRNTGQVVHLLLEKGQ VP
C-terminus from APC: KRHSGSYLVTSV

Data sets:

assigned_chemical_shifts
- shift_set_1
heteronucl_T1_relaxation
- T1_values
heteronucl_T2_relaxation
- T2_Values
heteronucl_NOEs
- heteronuclear_NOE

Data type	Count
13C chemical shifts	286
1H chemical shifts	632
15N chemical shifts	92
heteronuclear NOE values	81
T1 relaxation values	78
T2 relaxation values	78

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PDZ2 from PTP-BL	1

Entities:

Entity 1, PDZ2 from PTP-BL 102 residues - 9752.07 Da.

1

MET

HIS

MET

LYS

PRO

2

GLY

ASP

THR

PHE

GLU

VAL

GLU

LEU

ALA

LYS

3

THR

ASP

GLY

SER

LEU

GLY

ILE

SER

VAL

THR

4

GLY

VAL

ASN

THR

SER

VAL

ARG

HIS

GLY

5

GLY

ILE

TYR

VAL

LYS

ALA

ILE

PRO

LYS

6

GLY

ALA

GLU

SER

ASP

GLY

ARG

ILE

HIS

7

LYS

GLY

ASP

ARG

VAL

LEU

ALA

VAL

ASN

GLY

8

VAL

SER

LEU

GLU

GLY

ALA

THR

HIS

LYS

GLN

9

ALA

VAL

GLU

THR

LEU

ARG

ASN

THR

GLY

GLN

10

VAL

HIS

LEU

GLU

LYS

GLY

GLN

11

VAL

PRO

Samples:

sample_one: Second PDZ domain from PTP-BL, [U-2H; U-13C; U-15N], 1.0 mM; C-terminus from APC, [U-2H], 3 mM

conditions_1: pH: 6.8; temperature: 298 K; ionic strength: 0.1 M; pressure: 1 atm

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCA	sample_one	not available	conditions_1
3D HAHB(CO)NH	sample_one	not available	conditions_1
3D CCH	sample_one	not available	conditions_1
3D 13C NOESY HSQC (aliphatic)	sample_one	not available	conditions_1
3D 15N NOESY HSQC	sample_one	not available	conditions_1

Software:

NMRPipe v1.8 - spectral processing

XEASY v1.2 - peak integration, assignment

XPLOR v3.851 - simulated annealing, restrained MD refinement in water

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 800 MHz

GenBank	AAC42056 AAC42055
PDB	1VJ6 1GM1
BMRB	6092 6091 5131
AlphaFold	Q64499