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 19043

Title: Protein A binding by an engineered Affibody molecule   PubMed: 23924760

Authors: Hard, Torleif

Citation: Lindborg, Malin; Dubnovitsky, Anatoly; Olesen, Kenneth; Bjorkman, Tomas; Abrahmsen, Lars; Feldwisch, Joachim; Hard, Torleif. "High-affinity binding to staphylococcal protein A by an engineered dimeric Affibody molecule."  Protein Eng. Des. Sel. 26, 635-644 (2013).

Assembly members:
Z_domain, polymer, 58 residues, 6648.390 Da.
ZpA963, polymer, 58 residues, 6394.143 Da.

Natural source:   Common Name: Staphylococcus aureus   Taxonomy ID: 1280   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Staphylococcus aureus

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

Entity Sequences (FASTA):
Z_domain: VDNKFNKEQQNAFYEILHLP NLNEEQRNAFIQSLKDDPSQ SANLLAEAKKLNDAQAPK
ZpA963: VDNKFNKETQEASWEIFTLP NLNGRQVAAFISSLLDDPSQ SANLLAEAKKLNDAQAPK

Data sets:
Data typeCount
13C chemical shifts507
15N chemical shifts135
1H chemical shifts835

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Z_domain1
2ZpA9632

Entities:

Entity 1, Z_domain 58 residues - 6648.390 Da.

1   VALASPASNLYSPHEASNLYSGLUGLNGLN
2   ASNALAPHETYRGLUILELEUHISLEUPRO
3   ASNLEUASNGLUGLUGLNARGASNALAPHE
4   ILEGLNSERLEULYSASPASPPROSERGLN
5   SERALAASNLEULEUALAGLUALALYSLYS
6   LEUASNASPALAGLNALAPROLYS

Entity 2, ZpA963 58 residues - 6394.143 Da.

1   VALASPASNLYSPHEASNLYSGLUTHRGLN
2   GLUALASERTRPGLUILEPHETHRLEUPRO
3   ASNLEUASNGLYARGGLNVALALAALAPHE
4   ILESERSERLEULEUASPASPPROSERGLN
5   SERALAASNLEULEUALAGLUALALYSLYS
6   LEUASNASPALAGLNALAPROLYS

Samples:

sample_1: Z domain, [U-99% 13C; U-99% 15N], 0.5 – 1.0 mM; ZpA9630.625 – 1.25 mM; NaCl 75 mM; sodium phosphate 20 mM; azide 0.1%

sample_2: ZpA963, [U-99% 13C; U-99% 15N], 0.5 – 1.0 mM; Z domain0.625 – 1.25 mM; NaCl 75 mM; sodium phosphate 20 mM; azide 0.1%

sample_conditions_1: ionic strength: 0.095 M; pH: 5.6; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CACBsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D (HB)CB(CGCDCE)HEsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D F1(13C,15N)-filtered, F2(13C)-edited NOESYsample_1isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D HN(CO)CACBsample_2isotropicsample_conditions_1
3D 1H-15N TOCSYsample_2isotropicsample_conditions_1
3D HCCH-COSYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
2D (HB)CB(CGCDCE)HEsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_1
2D F1(13C,15N)-filtered, F2(13C)-edited NOESYsample_2isotropicsample_conditions_1

Software:

VNMR, Varian - collection

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

CcpNMR, CCPN - chemical shift assignment, data analysis, peak picking

DANGLE, Cheung MS, Maguire ML, Stevens TJ & Broadhurst RW (2010) J Magn Reson 202, 223-233. - data analysis

ARIA, Linge, O, . - structure solution

NMR spectrometers:

  • Varian INOVA 900 MHz
  • Varian INOVA 800 MHz

Related Database Links:

BMRB 4023
PDB
DBJ BAC76617 BAC76619 BAL27690 BAL27694 BAL27697
EMBL CAA49867 CAA65431
GB AAA72944 AAA73085 AAB00807 AAR10383 AAR10384
REF WP_052996913