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 6060

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)   PubMed: 14725761

Authors: Walma, Tine; Vuister, Geerten

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).

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

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

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

Data sets:
Data typeCount
13C chemical shifts286
1H chemical shifts632
15N chemical shifts92
heteronuclear NOE values81
T1 relaxation values78
T2 relaxation values78

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1PDZ2 from PTP-BL1

Entities:

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

1   METHISHISHISHISHISHISMETLYSPRO
2   GLYASPTHRPHEGLUVALGLULEUALALYS
3   THRASPGLYSERLEUGLYILESERVALTHR
4   GLYGLYVALASNTHRSERVALARGHISGLY
5   GLYILETYRVALLYSALAILEILEPROLYS
6   GLYALAALAGLUSERASPGLYARGILEHIS
7   LYSGLYASPARGVALLEUALAVALASNGLY
8   VALSERLEUGLUGLYALATHRHISLYSGLN
9   ALAVALGLUTHRLEUARGASNTHRGLYGLN
10   VALVALHISLEULEULEUGLULYSGLYGLN
11   VALPRO

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:

NameSampleSample stateSample conditions
3D HNCAsample_onenot availableconditions_1
3D HAHB(CO)NHsample_onenot availableconditions_1
3D CCHsample_onenot availableconditions_1
3D 13C NOESY HSQC (aliphatic)sample_onenot availableconditions_1
3D 15N NOESY HSQCsample_onenot availableconditions_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

Related Database Links:

GenBank AAC42056 AAC42055
PDB
BMRB 6092 6091 5131