BMRB Entry 15370

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15370
MolProbity Validation Chart

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Title:
solution structure of the atypical PDZ-like domain of synbindin
Deposition date:
2007-07-10
Original release date:
2009-04-24
Authors:
Feng, Yingang; Fan, Shilong; Gong, Weimin; Xia, Bin
Citation:

Citation: Fan, Shilong; Feng, Yingang; Wei, Zhiyi; Xia, Bin; Gong, Weimin. "Solution Structure of Synbindin Atypical PDZ Domain and Interaction with Syndecan-2"  Protein Pept. Lett. 16, 189-195 (2009).
PubMed: 19200043

Assembly members:

Assembly members:
apd, polymer, 96 residues, 10825.348 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET28

Entity Sequences (FASTA):

Entity Sequences (FASTA):
apd: MGHHHHHHLDSYAPRAEAEK TFSYPLDLLLKLHDERVLVA FGQRDGIRVGHAVLAINGMD VNGRYTADGKEVLEYLGNPA NYPVSIRFGRPRLTSN

Data sets:
Data typeCount
13C chemical shifts328
15N chemical shifts76
1H chemical shifts505

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1apd monomer1

Entities:

Entity 1, apd monomer 96 residues - 10825.348 Da.

1   METGLYHISHISHISHISHISHISLEUASP
2   SERTYRALAPROARGALAGLUALAGLULYS
3   THRPHESERTYRPROLEUASPLEULEULEU
4   LYSLEUHISASPGLUARGVALLEUVALALA
5   PHEGLYGLNARGASPGLYILEARGVALGLY
6   HISALAVALLEUALAILEASNGLYMETASP
7   VALASNGLYARGTYRTHRALAASPGLYLYS
8   GLUVALLEUGLUTYRLEUGLYASNPROALA
9   ASNTYRPROVALSERILEARGPHEGLYARG
10   PROARGLEUTHRSERASN

Samples:

sample_1: apd, [U-13C; U-15N], 1 – 1.5 mM; potassium phosphate 50 ± 1 mM; DSS 0.01%; sodium azide 0.01%

sample_conditions_1: ionic strength: 0.05 M; pH: 6.0; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
2D CB(CGCD)HDsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D CCH-TOCSYsample_1isotropicsample_conditions_1

Software:

xwinnmr, Bruker Biospin - collection

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

NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

SANE, Duggan, Legge, Dyson & Wright - refinement

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Koll - refinement

NMR spectrometers:

  • Bruker Avance 500 MHz

Related Database Links:

PDB
DBJ BAF83209
EMBL CAH91561
GB AAD34099 AAD44494 AAF21897 AAF29135 AAH10866
REF NP_001125918 NP_057230 XP_003253306 XP_003472832 XP_003820075
SP Q5R9J9 Q9Y296
AlphaFold Q5R9J9 Q9Y296

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks