BMRB Entry 11081

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11081
MolProbity Validation Chart

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Title:
Solution structure of the human DDEF1 SH3 domain
Deposition date:
2009-12-14
Original release date:
2011-05-19
Authors:
Kaieda, Shuji; Matsui, Chiyuki; Mimori-Kiyosue, Yuko; Ikegami, Takahisa
Citation:

Citation: Kaieda, Shuji; Matsui, Chiyuki; Mimori-Kiyosue, Yuko; Ikegami, Takahisa. "Structural basis of the recognition of the SAMP motif of adenomatous polyposis coli by the Src-homology 3 domain."  Biochemistry 49, 5143-5153 (2010).
PubMed: 20509626

Assembly members:

Assembly members:
DDEF1 SH3, polymer, 61 residues, 7066.874 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: pET32a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DDEF1 SH3: VRRVKTIYDCQADNDDELTF IEGEVIIVTGEEDQEWWIGH IEGQPERKGVFPVSFVHILS D

Data sets:
Data typeCount
13C chemical shifts279
15N chemical shifts60
1H chemical shifts423

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1DDEF1 SH31

Entities:

Entity 1, DDEF1 SH3 61 residues - 7066.874 Da.

1   VALARGARGVALLYSTHRILETYRASPCYS
2   GLNALAASPASNASPASPGLULEUTHRPHE
3   ILEGLUGLYGLUVALILEILEVALTHRGLY
4   GLUGLUASPGLNGLUTRPTRPILEGLYHIS
5   ILEGLUGLYGLNPROGLUARGLYSGLYVAL
6   PHEPROVALSERPHEVALHISILELEUSER
7   ASP

Samples:

sample_1: DDEF1 SH3, [U-15N], 0.7 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_2: DDEF1 SH3, [U-13C; U-15N], 0.7 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_3: DDEF1 SH3, [U-13C; U-15N], 0.7 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.02%; D2O 100%

sample_4: DDEF1 SH3, [U-15% 13C; U-15N], 0.7 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_conditions_1: pH: 7.2; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HN(CA)COsample_2isotropicsample_conditions_1
3D H(CCO)NHsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
3D 15N-edited NOESYsample_1isotropicsample_conditions_1
3D 13C-edited NOESYsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_4isotropicsample_conditions_1
2D 1H-13C CT-HSQCsample_4isotropicsample_conditions_1

Software:

xwinnmr v3.5, Bruker Biospin - collection

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

SPARKY v3.115, Goddard and Kneller - data analysis

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

ARIA v2.2, Rieping, Habeck, Bardiaux, Bernard, Malliavin, and Nilges - refinement

NMR spectrometers:

  • Bruker DRX 500 MHz
  • Bruker DRX 600 MHz
  • Bruker DRX 800 MHz

Related Database Links:

BMRB 11082 11153
PDB
DBJ BAA86563 BAC65759 BAE27250 BAE34783
EMBL CAD97831
GB AAB82338 AAC98349 AAC98350 AAH02201 AAH48818
REF NP_001037710 NP_001234925 NP_001263390 NP_001263391 NP_001263392
SP Q1AAU6 Q9QWY8 Q9ULH1
AlphaFold Q1AAU6 Q9QWY8 Q9ULH1

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